Starting phenix.real_space_refine
on Wed Mar  4 04:23:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kaq_22780/03_2026/7kaq_22780.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kaq_22780/03_2026/7kaq_22780.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/7kaq_22780/03_2026/7kaq_22780.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kaq_22780/03_2026/7kaq_22780.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kaq_22780/03_2026/7kaq_22780.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kaq_22780/03_2026/7kaq_22780.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=   0.064
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    7008      2.51       5
     N    1812      2.21       5
     O    1894      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10753
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 439, 3345
          Classifications: {'peptide': 439}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 19, 'TRANS': 419}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 108
          Unresolved non-hydrogen dihedrals: 75
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 4, 'TYR:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 69
    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: 3864
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 3864
          Classifications: {'peptide': 492}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 28, 'TRANS': 463}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 97
          Unresolved non-hydrogen angles: 122
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 1
          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
    Chain: "G"
      Number of atoms: 280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 280
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 56}
          Link IDs: {'TRANS': 55}
          Unresolved non-hydrogen bonds: 112
          Unresolved non-hydrogen angles: 168
          Unresolved non-hydrogen dihedrals: 56
          Planarities with less than four sites: {'UNK:plan-1': 56}
          Unresolved non-hydrogen planarities: 56
  Time building chain proxies: 2.74, per 1000 atoms: 0.25
  Number of scatterers: 10753
  At special positions: 0
  Unit cell: (108.1, 125.35, 135.7, 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    1894      8.00
     N    1812      7.00
     C    7008      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: 0.90
  Conformation dependent library (CDL) restraints added in 385.6 milliseconds
  

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2650

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 6 sheets defined
      71.3% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 47
    Processing helix  chain 'A' and resid 64 through 70
    Processing helix  chain 'A' and resid 82 through 98
    Processing helix  chain 'A' and resid 109 through 137
      removed outlier: 3.651A  pdb=" N   ILE A 124 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 174
      removed outlier: 3.838A  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 214 through 225
    Processing helix  chain 'A' and resid 227 through 238
      removed outlier: 3.946A  pdb=" N   VAL A 233 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   TYR A 237 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ARG A 238 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 262
      removed outlier: 3.560A  pdb=" N   VAL A 247 " --> pdb=" O   ASN A 243 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLY A 262 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 314
      removed outlier: 3.722A  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
    Processing helix  chain 'A' and resid 351 through 358
    Processing helix  chain 'A' and resid 358 through 384
      removed outlier: 3.696A  pdb=" N   THR A 367 " --> pdb=" O   ILE A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 399
    Processing helix  chain 'A' and resid 409 through 416
    Processing helix  chain 'A' and resid 417 through 440
    Processing helix  chain 'A' and resid 444 through 466
    Processing helix  chain 'C' and resid 27 through 39
    Processing helix  chain 'C' and resid 43 through 80
      removed outlier: 3.576A  pdb=" N   HIS C  72 " --> pdb=" O   ILE C  68 " (cutoff:3.500A)
      removed outlier: 4.050A  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
    Processing helix  chain 'D' and resid 13 through 36
      removed outlier: 3.588A  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 65
      removed outlier: 4.239A  pdb=" N   LEU D  62 " --> pdb=" O   VAL D  58 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   GLU D  64 " --> pdb=" O   LYS D  60 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLU D  65 " --> pdb=" O   ASN D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 68 through 78
    Processing helix  chain 'D' and resid 94 through 112
    Processing helix  chain 'D' and resid 212 through 217
    Processing helix  chain 'D' and resid 219 through 233
      removed outlier: 3.777A  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
      removed outlier: 3.645A  pdb=" N   ILE D 280 " --> pdb=" O   THR D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 287 through 294
      removed outlier: 3.855A  pdb=" N   LYS D 291 " --> pdb=" O   ALA D 287 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLN D 292 " --> pdb=" O   HIS D 288 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   PHE D 293 " --> pdb=" O   GLU D 289 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 311
    Processing helix  chain 'D' and resid 318 through 343
      removed outlier: 4.325A  pdb=" N   HIS D 330 " --> pdb=" O   VAL D 326 " (cutoff:3.500A)
      removed outlier: 5.435A  pdb=" N   SER D 331 " --> pdb=" O   ALA D 327 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LEU D 332 " --> pdb=" O   LYS D 328 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 345 through 362
      removed outlier: 3.756A  pdb=" N   ALA D 349 " --> pdb=" O   ASN D 345 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 378 through 386
      removed outlier: 4.066A  pdb=" N   THR D 384 " --> pdb=" O   GLU D 380 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 391 through 397
      removed outlier: 3.517A  pdb=" N   LEU D 395 " --> pdb=" O   THR D 391 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 399 through 408
      removed outlier: 3.606A  pdb=" N   GLY D 404 " --> pdb=" O   ASP D 400 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 411 through 423
      removed outlier: 4.079A  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 486
      removed outlier: 4.248A  pdb=" N   ASP D 486 " --> pdb=" O   GLU D 482 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 490 through 494
      removed outlier: 3.590A  pdb=" N   LYS D 493 " --> pdb=" O   MET D 490 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 537 through 545
      removed outlier: 6.777A  pdb=" N   ASP D 542 " --> pdb=" O   ASN D 539 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ASP D 543 " --> pdb=" O   LEU D 540 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LYS D 544 " --> pdb=" O   ASN D 541 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ASP D 545 " --> pdb=" O   ASP D 542 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 554 through 558
      removed outlier: 3.534A  pdb=" N   HIS D 558 " --> pdb=" O   LEU D 555 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 71 through 86
      removed outlier: 3.595A  pdb=" N   PHE E  76 " --> pdb=" O   HIS E  72 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ASN E  84 " --> pdb=" O   GLU E  80 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 89 through 123
      Proline residue:  E 115  - end of helix
    Processing helix  chain 'E' and resid 128 through 156
      removed outlier: 3.513A  pdb=" N   LYS E 132 " --> pdb=" O   GLU E 128 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   LYS E 139 " --> pdb=" O   GLU E 135 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLU E 142 " --> pdb=" O   VAL E 138 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 160 through 182
      removed outlier: 3.513A  pdb=" N   VAL E 164 " --> pdb=" O   VAL E 160 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   MET E 165 " --> pdb=" O   GLN E 161 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   PHE E 172 " --> pdb=" O   LYS E 168 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 182 through 195
      removed outlier: 4.123A  pdb=" N   GLU E 188 " --> pdb=" O   LEU E 184 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL E 189 " --> pdb=" O   LYS E 185 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   CYS E 190 " --> pdb=" O   ARG E 186 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ILE E 191 " --> pdb=" O   LYS E 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 199 through 203
      removed outlier: 3.589A  pdb=" N   GLY E 202 " --> pdb=" O   ASN E 199 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 21 through 41
    Processing helix  chain 'F' and resid 52 through 71
      removed outlier: 3.808A  pdb=" N   ASN F  68 " --> pdb=" O   SER F  64 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   LEU F  69 " --> pdb=" O   GLY F  65 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLN F  70 " --> pdb=" O   MET F  66 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 75 through 91
    Processing helix  chain 'F' and resid 97 through 120
      Proline residue:  F 103  - end of helix
    Processing helix  chain 'F' and resid 122 through 135
    Processing helix  chain 'F' and resid 139 through 153
      removed outlier: 3.631A  pdb=" N   PHE F 143 " --> pdb=" O   GLN F 139 " (cutoff:3.500A)
      removed outlier: 4.236A  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 174 through 192
      removed outlier: 3.619A  pdb=" N   ALA F 178 " --> pdb=" O   MET F 174 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 151 through 170
      removed outlier: 3.640A  pdb=" N   UNK G 170 " --> pdb=" O   UNK G 166 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 175 through 205
    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 278 through 284
    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: 6.805A  pdb=" N   LYS D 454 " --> pdb=" O   ILE D 431 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   ALA D 433 " --> pdb=" O   SER D 452 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   SER D 452 " --> pdb=" O   ALA D 433 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   PHE D 435 " --> pdb=" O   TYR D 450 " (cutoff:3.500A)
      removed outlier: 6.377A  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

    705 hydrogen bonds defined for protein.
    2070 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: 1.60

  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: 3404
        1.34 -     1.46: 2126
        1.46 -     1.57: 5370
        1.57 -     1.69: 0
        1.69 -     1.81: 61
  Bond restraints: 10961
  Sorted by residual:
  bond pdb=" C   LYS D 493 "
       pdb=" N   GLN D 494 "
    ideal  model  delta    sigma   weight residual
    1.331  1.305  0.026 2.83e-02 1.25e+03 8.58e-01
  bond pdb=" CA  LEU F 102 "
       pdb=" C   LEU F 102 "
    ideal  model  delta    sigma   weight residual
    1.521  1.529 -0.008 1.14e-02 7.69e+03 5.47e-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 5.27e-01
  bond pdb=" C   GLU D  12 "
       pdb=" N   THR D  13 "
    ideal  model  delta    sigma   weight residual
    1.332  1.322  0.010 1.40e-02 5.10e+03 5.27e-01
  bond pdb=" CB  VAL C  54 "
       pdb=" CG1 VAL C  54 "
    ideal  model  delta    sigma   weight residual
    1.521  1.497  0.024 3.30e-02 9.18e+02 5.09e-01
  ... (remaining 10956 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 14726
        1.91 -     3.81: 123
        3.81 -     5.72: 18
        5.72 -     7.63: 5
        7.63 -     9.53: 1
  Bond angle restraints: 14873
  Sorted by residual:
  angle pdb=" C   ILE A 417 "
        pdb=" N   ILE A 418 "
        pdb=" CA  ILE A 418 "
      ideal   model   delta    sigma   weight residual
     120.33  122.46   -2.13 8.00e-01 1.56e+00 7.11e+00
  angle pdb=" N   PRO D 426 "
        pdb=" CA  PRO D 426 "
        pdb=" C   PRO D 426 "
      ideal   model   delta    sigma   weight residual
     110.55  114.48   -3.93 1.63e+00 3.76e-01 5.80e+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  110.93    3.07 1.31e+00 5.83e-01 5.48e+00
  angle pdb=" N   VAL D  25 "
        pdb=" CA  VAL D  25 "
        pdb=" C   VAL D  25 "
      ideal   model   delta    sigma   weight residual
     111.81  109.93    1.88 8.60e-01 1.35e+00 4.79e+00
  angle pdb=" C   PRO D 471 "
        pdb=" N   GLU D 472 "
        pdb=" CA  GLU D 472 "
      ideal   model   delta    sigma   weight residual
     121.54  125.52   -3.98 1.91e+00 2.74e-01 4.35e+00
  ... (remaining 14868 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 6189
       17.67 -    35.33: 338
       35.33 -    53.00: 54
       53.00 -    70.67: 5
       70.67 -    88.33: 9
  Dihedral angle restraints: 6595
    sinusoidal: 2518
      harmonic: 4077
  Sorted by residual:
  dihedral pdb=" CA  SER A 289 "
           pdb=" C   SER A 289 "
           pdb=" N   ASN A 290 "
           pdb=" CA  ASN A 290 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.74   16.26     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CB  GLU E 144 "
           pdb=" CG  GLU E 144 "
           pdb=" CD  GLU E 144 "
           pdb=" OE1 GLU E 144 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.33   88.33     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CB  GLU F  63 "
           pdb=" CG  GLU F  63 "
           pdb=" CD  GLU F  63 "
           pdb=" OE1 GLU F  63 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.00   88.00     1      3.00e+01 1.11e-03 1.03e+01
  ... (remaining 6592 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1075
       0.027 -    0.054: 452
       0.054 -    0.080: 160
       0.080 -    0.107: 78
       0.107 -    0.134: 12
  Chirality restraints: 1777
  Sorted by residual:
  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    2.57   -0.13 2.00e-01 2.50e+01 4.48e-01
  chirality pdb=" CB  THR D 448 "
            pdb=" CA  THR D 448 "
            pdb=" OG1 THR D 448 "
            pdb=" CG2 THR D 448 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.42    0.13 2.00e-01 2.50e+01 4.33e-01
  chirality pdb=" CA  SER A  83 "
            pdb=" N   SER A  83 "
            pdb=" C   SER A  83 "
            pdb=" CB  SER A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.73e-01
  ... (remaining 1774 not shown)

  Planarity restraints: 1855
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR F  47 "    0.027 5.00e-02 4.00e+02   4.09e-02 2.68e+00
        pdb=" N   PRO F  48 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO F  48 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO F  48 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D 462 "   -0.018 5.00e-02 4.00e+02   2.66e-02 1.13e+00
        pdb=" N   PRO D 463 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO D 463 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO D 463 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA F  93 "   -0.017 5.00e-02 4.00e+02   2.52e-02 1.01e+00
        pdb=" N   PRO F  94 "    0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO F  94 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO F  94 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 1852 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 287
        2.71 -     3.25: 11487
        3.25 -     3.80: 17396
        3.80 -     4.35: 20289
        4.35 -     4.90: 34815
  Nonbonded interactions: 84274
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 287 "
            pdb=" OG1 THR A 386 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" OG  SER A  72 "
            pdb=" O   LEU A  78 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" NH1 ARG F  92 "
            pdb=" OE1 GLU F  96 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" O   THR D 444 "
            pdb=" OG  SER D 447 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   PHE A 198 "
            pdb=" OH  TYR C  66 "
     model   vdw
     2.252 3.040
  ... (remaining 84269 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:             1.740
  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:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.380
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
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   0.026  10961  Z= 0.134
  Angle     :  0.521   9.533  14873  Z= 0.290
  Chirality :  0.037   0.134   1777
  Planarity :  0.003   0.041   1855
  Dihedral  : 11.528  88.332   3945
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.00 (0.22), residues: 1322
  helix:  0.29 (0.17), residues: 833
  sheet: -2.85 (0.44), residues: 84
  loop : -2.05 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 145 
 TYR   0.011   0.001   TYR F 190 
 PHE   0.012   0.001   PHE A  92 
 TRP   0.009   0.001   TRP A 380 
 HIS   0.003   0.001   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (10961)
  covalent geometry    : angle       0.52142 (14873)
  hydrogen bonds       : bond        0.13071 (  705)
  hydrogen bonds       : angle       4.94118 ( 2070)

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

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.7945 (m-90) cc_final: 0.7212 (t-100)
REVERT: A  131 LEU cc_start: 0.9711 (mm) cc_final: 0.9365 (pp)
REVERT: A  158 MET cc_start: 0.9212 (ppp) cc_final: 0.9004 (ppp)
REVERT: A  191 GLU cc_start: 0.9306 (tt0) cc_final: 0.9081 (pp20)
REVERT: A  400 MET cc_start: 0.9222 (mmm) cc_final: 0.8813 (tpp)
REVERT: C   43 ASP cc_start: 0.9311 (p0) cc_final: 0.9044 (p0)
REVERT: C   46 GLU cc_start: 0.9278 (tt0) cc_final: 0.8797 (pt0)
REVERT: E   81 MET cc_start: 0.8987 (ttm) cc_final: 0.8682 (tpp)
REVERT: E  121 TYR cc_start: 0.8786 (t80) cc_final: 0.8499 (t80)
REVERT: E  141 ILE cc_start: 0.9618 (mm) cc_final: 0.9387 (tp)
REVERT: F   66 MET cc_start: 0.9593 (mmm) cc_final: 0.9334 (mmm)
REVERT: F   87 MET cc_start: 0.9481 (ttp) cc_final: 0.9064 (tmm)
REVERT: F  101 GLN cc_start: 0.8733 (tt0) cc_final: 0.8382 (mt0)
REVERT: F  107 PHE cc_start: 0.8621 (t80) cc_final: 0.8220 (t80)
REVERT: F  128 ASP cc_start: 0.9128 (m-30) cc_final: 0.8846 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.0996
  time to fit residues: 19.4635
Evaluate side-chains
  81 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 98 optimal weight:    0.0570
   chunk 107 optimal weight:    0.5980
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.0970
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    0.7500

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
A 394 GLN
A 398 GLN
D 307 GLN
D 494 GLN
D 558 HIS
E  88 HIS
F  68 ASN
F 106 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.048781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.037578 restraints weight = 76393.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.038697 restraints weight = 40932.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.039418 restraints weight = 27058.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.039969 restraints weight = 20370.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.040257 restraints weight = 16655.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10961  Z= 0.104
  Angle     :  0.551  12.876  14873  Z= 0.262
  Chirality :  0.039   0.202   1777
  Planarity :  0.003   0.038   1855
  Dihedral  :  3.093  15.133   1480
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 10.37 %
    Favored  : 89.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.23), residues: 1322
  helix:  1.43 (0.18), residues: 838
  sheet: -2.43 (0.44), residues: 90
  loop : -1.55 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  90 
 TYR   0.009   0.001   TYR F 190 
 PHE   0.021   0.001   PHE B  64 
 TRP   0.007   0.001   TRP F  95 
 HIS   0.002   0.001   HIS D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 (10961)
  covalent geometry    : angle       0.55066 (14873)
  hydrogen bonds       : bond        0.03204 (  705)
  hydrogen bonds       : angle       3.90071 ( 2070)

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

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.8045 (m-90) cc_final: 0.7251 (t-100)
REVERT: A  131 LEU cc_start: 0.9546 (mm) cc_final: 0.9319 (pp)
REVERT: A  158 MET cc_start: 0.9072 (ppp) cc_final: 0.8612 (mmt)
REVERT: A  290 ASN cc_start: 0.8281 (t0) cc_final: 0.8068 (t0)
REVERT: A  337 MET cc_start: 0.8741 (mpp) cc_final: 0.8390 (pmm)
REVERT: A  400 MET cc_start: 0.9062 (mmm) cc_final: 0.8820 (tpp)
REVERT: C   43 ASP cc_start: 0.9184 (p0) cc_final: 0.8855 (p0)
REVERT: C   46 GLU cc_start: 0.9176 (tt0) cc_final: 0.8885 (pt0)
REVERT: C   56 ILE cc_start: 0.8803 (mm) cc_final: 0.8556 (pt)
REVERT: E  141 ILE cc_start: 0.9575 (mm) cc_final: 0.9374 (tp)
REVERT: E  165 MET cc_start: 0.8508 (ttp) cc_final: 0.8183 (ppp)
REVERT: E  200 ASN cc_start: 0.9401 (t0) cc_final: 0.9150 (t0)
REVERT: F   66 MET cc_start: 0.9512 (mmm) cc_final: 0.9310 (mmp)
REVERT: F   87 MET cc_start: 0.9268 (ttp) cc_final: 0.8367 (ttp)
REVERT: F  107 PHE cc_start: 0.8458 (t80) cc_final: 0.8035 (t80)
REVERT: F  114 ASP cc_start: 0.9235 (m-30) cc_final: 0.8960 (p0)
REVERT: F  128 ASP cc_start: 0.9104 (m-30) cc_final: 0.8798 (m-30)
  outliers start: 7
  outliers final: 4
  residues processed: 95
  average time/residue: 0.0774
  time to fit residues: 11.7042
Evaluate side-chains
  82 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain E residue  201 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 132 optimal weight:   40.0000
   chunk 4 optimal weight:    3.9990
   chunk 47 optimal weight:    8.9990
   chunk 18 optimal weight:    5.9990
   chunk 61 optimal weight:    9.9990
   chunk 124 optimal weight:    4.9990
   chunk 128 optimal weight:    7.9990
   chunk 15 optimal weight:    9.9990
   chunk 56 optimal weight:   10.0000
   chunk 113 optimal weight:   20.0000
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 290 ASN
A 347 GLN
D 288 HIS
D 334 HIS
E  98 ASN
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.046457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.035225 restraints weight = 78623.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.036233 restraints weight = 42784.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.036897 restraints weight = 28654.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.037332 restraints weight = 21809.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.037677 restraints weight = 18236.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  10961  Z= 0.271
  Angle     :  0.674  13.181  14873  Z= 0.331
  Chirality :  0.041   0.216   1777
  Planarity :  0.004   0.041   1855
  Dihedral  :  3.516  18.324   1480
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 13.32 %
    Favored  : 85.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.24), residues: 1322
  helix:  1.75 (0.18), residues: 832
  sheet: -1.81 (0.48), residues: 90
  loop : -1.25 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  90 
 TYR   0.024   0.002   TYR E 121 
 PHE   0.021   0.002   PHE B  64 
 TRP   0.012   0.002   TRP D 513 
 HIS   0.011   0.002   HIS D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00578 (10961)
  covalent geometry    : angle       0.67431 (14873)
  hydrogen bonds       : bond        0.03470 (  705)
  hydrogen bonds       : angle       4.18400 ( 2070)

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

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.8125 (m-90) cc_final: 0.7249 (t-100)
REVERT: A  131 LEU cc_start: 0.9549 (mm) cc_final: 0.9302 (pp)
REVERT: A  158 MET cc_start: 0.9118 (ppp) cc_final: 0.8885 (ppp)
REVERT: A  290 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.8237 (t0)
REVERT: A  337 MET cc_start: 0.8768 (mpp) cc_final: 0.8517 (pmm)
REVERT: B   58 LEU cc_start: 0.8898 (tt) cc_final: 0.8689 (tt)
REVERT: B   59 PHE cc_start: 0.8642 (m-10) cc_final: 0.7438 (t80)
REVERT: D  606 MET cc_start: 0.8842 (mtm) cc_final: 0.8607 (ptp)
REVERT: F   66 MET cc_start: 0.9578 (mmm) cc_final: 0.9341 (mmm)
REVERT: F   87 MET cc_start: 0.9133 (ttp) cc_final: 0.8846 (ttp)
REVERT: F  108 MET cc_start: 0.9516 (mpp) cc_final: 0.9308 (mpp)
REVERT: F  114 ASP cc_start: 0.9222 (m-30) cc_final: 0.8952 (p0)
  outliers start: 16
  outliers final: 11
  residues processed: 86
  average time/residue: 0.0701
  time to fit residues: 9.8742
Evaluate side-chains
  79 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain D residue  448 THR
Chi-restraints excluded: chain D residue  514 CYS
Chi-restraints excluded: chain E residue  201 ASP
Chi-restraints excluded: chain F residue   71 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 105 optimal weight:    0.9980
   chunk 127 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 118 optimal weight:    8.9990
   chunk 82 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9980
   chunk 18 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 114 optimal weight:   10.0000
   chunk 85 optimal weight:    2.9990
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 290 ASN
D 330 HIS
E  98 ASN
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 174 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.047660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.036373 restraints weight = 77617.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.037427 restraints weight = 42486.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.038154 restraints weight = 28432.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.038605 restraints weight = 21594.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.038859 restraints weight = 18017.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10961  Z= 0.110
  Angle     :  0.565  12.794  14873  Z= 0.266
  Chirality :  0.039   0.234   1777
  Planarity :  0.003   0.038   1855
  Dihedral  :  3.301  16.990   1480
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 14.57 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.24), residues: 1322
  helix:  2.01 (0.18), residues: 838
  sheet: -1.48 (0.49), residues: 88
  loop : -0.95 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  90 
 TYR   0.019   0.001   TYR E 121 
 PHE   0.020   0.001   PHE B  66 
 TRP   0.009   0.001   TRP A 380 
 HIS   0.003   0.001   HIS D 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (10961)
  covalent geometry    : angle       0.56453 (14873)
  hydrogen bonds       : bond        0.03098 (  705)
  hydrogen bonds       : angle       3.78336 ( 2070)

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

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.8223 (m-90) cc_final: 0.7284 (t-100)
REVERT: A  131 LEU cc_start: 0.9571 (mm) cc_final: 0.9323 (pp)
REVERT: A  158 MET cc_start: 0.9096 (ppp) cc_final: 0.8871 (ppp)
REVERT: A  337 MET cc_start: 0.8798 (mpp) cc_final: 0.8533 (pmm)
REVERT: C   56 ILE cc_start: 0.8834 (mm) cc_final: 0.8579 (pt)
REVERT: D  606 MET cc_start: 0.8843 (mtm) cc_final: 0.8553 (ptp)
REVERT: E  165 MET cc_start: 0.8687 (ttp) cc_final: 0.8135 (ppp)
REVERT: F   66 MET cc_start: 0.9571 (mmm) cc_final: 0.9312 (mmp)
REVERT: F  108 MET cc_start: 0.9475 (OUTLIER) cc_final: 0.9151 (mpp)
REVERT: F  114 ASP cc_start: 0.9185 (m-30) cc_final: 0.8894 (p0)
  outliers start: 16
  outliers final: 8
  residues processed: 87
  average time/residue: 0.0658
  time to fit residues: 9.4941
Evaluate side-chains
  77 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain D residue  448 THR
Chi-restraints excluded: chain D residue  599 THR
Chi-restraints excluded: chain E residue  171 CYS
Chi-restraints excluded: chain E residue  201 ASP
Chi-restraints excluded: chain F residue  108 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 91 optimal weight:    0.2980
   chunk 36 optimal weight:    6.9990
   chunk 88 optimal weight:    6.9990
   chunk 113 optimal weight:    4.9990
   chunk 38 optimal weight:    7.9990
   chunk 67 optimal weight:    3.9990
   chunk 124 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 128 optimal weight:    5.9990
   overall best weight:    2.6588

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 173 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 = 0.3086 r_free = 0.3086 target = 0.047039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.035847 restraints weight = 77245.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2740 r_free = 0.2740 target = 0.036844 restraints weight = 42560.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.037566 restraints weight = 28735.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.038006 restraints weight = 21812.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.038273 restraints weight = 18236.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10961  Z= 0.153
  Angle     :  0.575  12.291  14873  Z= 0.276
  Chirality :  0.039   0.237   1777
  Planarity :  0.003   0.040   1855
  Dihedral  :  3.319  20.969   1480
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.64 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.24), residues: 1322
  helix:  2.14 (0.18), residues: 838
  sheet: -1.23 (0.51), residues: 88
  loop : -0.78 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  92 
 TYR   0.019   0.001   TYR E 121 
 PHE   0.012   0.001   PHE B  64 
 TRP   0.009   0.001   TRP F  95 
 HIS   0.004   0.001   HIS E  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (10961)
  covalent geometry    : angle       0.57486 (14873)
  hydrogen bonds       : bond        0.03047 (  705)
  hydrogen bonds       : angle       3.82565 ( 2070)

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

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.8344 (m-90) cc_final: 0.7378 (t-100)
REVERT: A  131 LEU cc_start: 0.9571 (mm) cc_final: 0.9323 (pp)
REVERT: A  158 MET cc_start: 0.9156 (ppp) cc_final: 0.8923 (ppp)
REVERT: A  337 MET cc_start: 0.8839 (mpp) cc_final: 0.8577 (pmm)
REVERT: A  400 MET cc_start: 0.9013 (tpp) cc_final: 0.8760 (tpp)
REVERT: F   66 MET cc_start: 0.9603 (mmm) cc_final: 0.9348 (mmp)
REVERT: F  108 MET cc_start: 0.9490 (OUTLIER) cc_final: 0.9283 (mpp)
  outliers start: 18
  outliers final: 10
  residues processed: 83
  average time/residue: 0.0804
  time to fit residues: 10.7133
Evaluate side-chains
  79 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain D residue  280 ILE
Chi-restraints excluded: chain D residue  448 THR
Chi-restraints excluded: chain D residue  599 THR
Chi-restraints excluded: chain E residue  171 CYS
Chi-restraints excluded: chain E residue  201 ASP
Chi-restraints excluded: chain F residue  108 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 124 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 6 optimal weight:    7.9990
   chunk 114 optimal weight:   20.0000
   chunk 63 optimal weight:    8.9990
   chunk 100 optimal weight:   10.0000
   chunk 109 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   chunk 15 optimal weight:   10.0000
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 539 ASN
E  98 ASN
** E 173 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 = 0.3046 r_free = 0.3046 target = 0.045758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.034679 restraints weight = 78718.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.035628 restraints weight = 42768.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.036310 restraints weight = 28962.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.036712 restraints weight = 22061.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.037086 restraints weight = 18504.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  10961  Z= 0.266
  Angle     :  0.681  12.876  14873  Z= 0.333
  Chirality :  0.041   0.226   1777
  Planarity :  0.004   0.038   1855
  Dihedral  :  3.664  20.816   1480
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 15.82 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.24), residues: 1322
  helix:  2.00 (0.18), residues: 836
  sheet: -1.13 (0.54), residues: 84
  loop : -0.71 (0.33), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  90 
 TYR   0.057   0.002   TYR E 121 
 PHE   0.028   0.002   PHE B  64 
 TRP   0.010   0.002   TRP F  95 
 HIS   0.008   0.002   HIS E  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00568 (10961)
  covalent geometry    : angle       0.68062 (14873)
  hydrogen bonds       : bond        0.03460 (  705)
  hydrogen bonds       : angle       4.17996 ( 2070)

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

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 64
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.8353 (m-90) cc_final: 0.7577 (t-100)
REVERT: A  131 LEU cc_start: 0.9559 (mm) cc_final: 0.9310 (pp)
REVERT: A  158 MET cc_start: 0.9152 (ppp) cc_final: 0.8889 (ppp)
REVERT: A  337 MET cc_start: 0.8867 (mpp) cc_final: 0.8653 (pmm)
REVERT: A  400 MET cc_start: 0.8976 (tpp) cc_final: 0.8673 (tpp)
REVERT: B   59 PHE cc_start: 0.8616 (m-10) cc_final: 0.7352 (t80)
REVERT: E  121 TYR cc_start: 0.8728 (t80) cc_final: 0.8514 (t80)
REVERT: E  165 MET cc_start: 0.8820 (ttp) cc_final: 0.8456 (ppp)
REVERT: F   66 MET cc_start: 0.9591 (mmm) cc_final: 0.9247 (mmm)
REVERT: F  108 MET cc_start: 0.9509 (OUTLIER) cc_final: 0.9299 (mpp)
REVERT: F  114 ASP cc_start: 0.9236 (m-30) cc_final: 0.8943 (p0)
  outliers start: 27
  outliers final: 16
  residues processed: 86
  average time/residue: 0.0805
  time to fit residues: 10.9350
Evaluate side-chains
  80 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain D residue  280 ILE
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  443 VAL
Chi-restraints excluded: chain D residue  448 THR
Chi-restraints excluded: chain D residue  474 ASN
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  599 THR
Chi-restraints excluded: chain E residue  171 CYS
Chi-restraints excluded: chain E residue  201 ASP
Chi-restraints excluded: chain F residue  108 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 50 optimal weight:    4.9990
   chunk 105 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 92 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 89 optimal weight:    3.9990
   chunk 117 optimal weight:    1.9990
   chunk 132 optimal weight:   40.0000
   chunk 126 optimal weight:    5.9990
   chunk 114 optimal weight:    5.9990
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 173 ASN ** 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 = 0.3085 r_free = 0.3085 target = 0.046939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.035840 restraints weight = 76523.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2740 r_free = 0.2740 target = 0.036837 restraints weight = 41851.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.037540 restraints weight = 28163.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.038032 restraints weight = 21414.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.038307 restraints weight = 17720.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10961  Z= 0.124
  Angle     :  0.580  12.159  14873  Z= 0.276
  Chirality :  0.039   0.257   1777
  Planarity :  0.003   0.036   1855
  Dihedral  :  3.412  20.533   1480
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 16.44 %
    Favored  : 81.95 %
  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 are not related in a simple way.
  whole:  1.77 (0.24), residues: 1322
  helix:  2.20 (0.18), residues: 844
  sheet: -0.94 (0.53), residues: 88
  loop : -0.59 (0.34), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  90 
 TYR   0.035   0.001   TYR E 121 
 PHE   0.022   0.001   PHE B  64 
 TRP   0.010   0.001   TRP A 380 
 HIS   0.003   0.001   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (10961)
  covalent geometry    : angle       0.57955 (14873)
  hydrogen bonds       : bond        0.03069 (  705)
  hydrogen bonds       : angle       3.79783 ( 2070)

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

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.8398 (m-90) cc_final: 0.7518 (t-100)
REVERT: A  131 LEU cc_start: 0.9553 (mm) cc_final: 0.9327 (pp)
REVERT: A  158 MET cc_start: 0.9149 (ppp) cc_final: 0.8876 (ppp)
REVERT: A  165 MET cc_start: 0.9447 (ppp) cc_final: 0.9112 (ppp)
REVERT: A  337 MET cc_start: 0.8866 (mpp) cc_final: 0.8495 (pmm)
REVERT: A  400 MET cc_start: 0.9021 (tpp) cc_final: 0.8671 (tpp)
REVERT: B   59 PHE cc_start: 0.8583 (m-10) cc_final: 0.7404 (t80)
REVERT: E   81 MET cc_start: 0.8996 (ttm) cc_final: 0.8727 (tpp)
REVERT: E  165 MET cc_start: 0.8741 (ttp) cc_final: 0.8147 (ppp)
REVERT: F   66 MET cc_start: 0.9573 (mmm) cc_final: 0.9336 (mmp)
REVERT: F  108 MET cc_start: 0.9499 (OUTLIER) cc_final: 0.9192 (mpp)
REVERT: F  114 ASP cc_start: 0.9224 (m-30) cc_final: 0.8970 (p0)
  outliers start: 18
  outliers final: 13
  residues processed: 83
  average time/residue: 0.0732
  time to fit residues: 9.8309
Evaluate side-chains
  77 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain D residue  280 ILE
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  448 THR
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  599 THR
Chi-restraints excluded: chain E residue  171 CYS
Chi-restraints excluded: chain E residue  201 ASP
Chi-restraints excluded: chain F residue  108 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 79 optimal weight:    0.0980
   chunk 69 optimal weight:    5.9990
   chunk 55 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 3 optimal weight:    3.9990
   chunk 9 optimal weight:    9.9990
   chunk 135 optimal weight:   40.0000
   chunk 77 optimal weight:    6.9990
   chunk 66 optimal weight:    0.3980
   chunk 18 optimal weight:    3.9990
   chunk 31 optimal weight:   10.0000
   overall best weight:    2.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  98 ASN
** E 173 ASN ** 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 = 0.3076 r_free = 0.3076 target = 0.046648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.035697 restraints weight = 76852.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.036630 restraints weight = 43221.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.037304 restraints weight = 29569.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.037791 restraints weight = 22656.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.038035 restraints weight = 18811.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.3111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10961  Z= 0.166
  Angle     :  0.621  11.990  14873  Z= 0.298
  Chirality :  0.040   0.255   1777
  Planarity :  0.003   0.035   1855
  Dihedral  :  3.426  19.484   1480
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 16.53 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.79 (0.24), residues: 1322
  helix:  2.20 (0.18), residues: 843
  sheet: -0.92 (0.54), residues: 88
  loop : -0.57 (0.33), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  90 
 TYR   0.022   0.001   TYR E 121 
 PHE   0.020   0.001   PHE B  64 
 TRP   0.011   0.001   TRP F  95 
 HIS   0.004   0.001   HIS E  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (10961)
  covalent geometry    : angle       0.62055 (14873)
  hydrogen bonds       : bond        0.03143 (  705)
  hydrogen bonds       : angle       3.88048 ( 2070)

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

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 62
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.8377 (m-90) cc_final: 0.7498 (t-100)
REVERT: A  131 LEU cc_start: 0.9517 (mm) cc_final: 0.9291 (pp)
REVERT: A  158 MET cc_start: 0.9095 (ppp) cc_final: 0.8867 (ppp)
REVERT: A  337 MET cc_start: 0.8860 (mpp) cc_final: 0.8486 (pmm)
REVERT: B   59 PHE cc_start: 0.8564 (m-10) cc_final: 0.7485 (t80)
REVERT: E  165 MET cc_start: 0.8827 (ttp) cc_final: 0.8406 (ppp)
REVERT: F  114 ASP cc_start: 0.9161 (m-30) cc_final: 0.8900 (p0)
  outliers start: 22
  outliers final: 15
  residues processed: 79
  average time/residue: 0.0789
  time to fit residues: 10.2168
Evaluate side-chains
  75 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain D residue  280 ILE
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  448 THR
Chi-restraints excluded: chain D residue  514 CYS
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  599 THR
Chi-restraints excluded: chain E residue  171 CYS
Chi-restraints excluded: chain E residue  201 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 117 optimal weight:   40.0000
   chunk 135 optimal weight:   40.0000
   chunk 11 optimal weight:    6.9990
   chunk 104 optimal weight:    0.7980
   chunk 128 optimal weight:    6.9990
   chunk 70 optimal weight:    9.9990
   chunk 99 optimal weight:    2.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 173 ASN ** 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 = 0.3080 r_free = 0.3080 target = 0.046795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.035661 restraints weight = 76785.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.036629 restraints weight = 42250.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.037332 restraints weight = 28715.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.037758 restraints weight = 21829.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.038122 restraints weight = 18242.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.3215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10961  Z= 0.146
  Angle     :  0.640  12.496  14873  Z= 0.301
  Chirality :  0.039   0.263   1777
  Planarity :  0.003   0.035   1855
  Dihedral  :  3.400  19.128   1480
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 17.16 %
    Favored  : 81.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.82 (0.24), residues: 1322
  helix:  2.20 (0.18), residues: 844
  sheet: -0.93 (0.54), residues: 88
  loop : -0.48 (0.34), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  90 
 TYR   0.021   0.001   TYR E 121 
 PHE   0.019   0.001   PHE B  64 
 TRP   0.015   0.001   TRP E 131 
 HIS   0.003   0.001   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (10961)
  covalent geometry    : angle       0.63971 (14873)
  hydrogen bonds       : bond        0.03109 (  705)
  hydrogen bonds       : angle       3.81873 ( 2070)

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

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.8444 (m-90) cc_final: 0.7510 (t-100)
REVERT: A  131 LEU cc_start: 0.9560 (mm) cc_final: 0.9317 (pp)
REVERT: A  158 MET cc_start: 0.9158 (ppp) cc_final: 0.8889 (ppp)
REVERT: A  337 MET cc_start: 0.8885 (mpp) cc_final: 0.8401 (pmm)
REVERT: B   59 PHE cc_start: 0.8617 (m-10) cc_final: 0.7481 (t80)
REVERT: E   81 MET cc_start: 0.8992 (ttm) cc_final: 0.8691 (tpp)
REVERT: E  165 MET cc_start: 0.8798 (ttp) cc_final: 0.8344 (ppp)
REVERT: F  108 MET cc_start: 0.9330 (mpp) cc_final: 0.9032 (mpp)
REVERT: F  114 ASP cc_start: 0.9220 (m-30) cc_final: 0.8973 (p0)
  outliers start: 18
  outliers final: 15
  residues processed: 79
  average time/residue: 0.0862
  time to fit residues: 10.7650
Evaluate side-chains
  78 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue  280 ILE
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  448 THR
Chi-restraints excluded: chain D residue  514 CYS
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  599 THR
Chi-restraints excluded: chain E residue  171 CYS
Chi-restraints excluded: chain E residue  201 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 85 optimal weight:    0.5980
   chunk 95 optimal weight:    8.9990
   chunk 7 optimal weight:    4.9990
   chunk 129 optimal weight:    7.9990
   chunk 8 optimal weight:   30.0000
   chunk 64 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 122 optimal weight:    0.0370
   overall best weight:    2.9264

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 206 HIS
** E 173 ASN ** 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 = 0.3074 r_free = 0.3074 target = 0.046625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.035572 restraints weight = 77818.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.036511 restraints weight = 43974.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.037186 restraints weight = 30107.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.037585 restraints weight = 23164.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.037941 restraints weight = 19442.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.3347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10961  Z= 0.168
  Angle     :  0.672  19.392  14873  Z= 0.315
  Chirality :  0.040   0.256   1777
  Planarity :  0.003   0.035   1855
  Dihedral  :  3.436  18.820   1480
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 17.07 %
    Favored  : 81.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.24), residues: 1322
  helix:  2.14 (0.18), residues: 849
  sheet: -0.91 (0.55), residues: 88
  loop : -0.53 (0.34), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  90 
 TYR   0.020   0.001   TYR E 121 
 PHE   0.019   0.001   PHE B  64 
 TRP   0.015   0.001   TRP E 131 
 HIS   0.004   0.001   HIS E  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (10961)
  covalent geometry    : angle       0.67219 (14873)
  hydrogen bonds       : bond        0.03194 (  705)
  hydrogen bonds       : angle       3.90809 ( 2070)

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

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.8493 (m-90) cc_final: 0.7666 (t60)
REVERT: A  131 LEU cc_start: 0.9557 (mm) cc_final: 0.9310 (pp)
REVERT: A  158 MET cc_start: 0.9135 (ppp) cc_final: 0.8874 (ppp)
REVERT: A  165 MET cc_start: 0.9424 (ppp) cc_final: 0.9103 (ppp)
REVERT: A  337 MET cc_start: 0.8901 (mpp) cc_final: 0.8441 (pmm)
REVERT: A  400 MET cc_start: 0.8988 (tpp) cc_final: 0.8726 (tpp)
REVERT: B   59 PHE cc_start: 0.8588 (m-10) cc_final: 0.7462 (t80)
REVERT: E  165 MET cc_start: 0.8857 (ttp) cc_final: 0.8410 (ppp)
REVERT: F  108 MET cc_start: 0.9323 (mpp) cc_final: 0.9025 (mpp)
REVERT: F  114 ASP cc_start: 0.9194 (m-30) cc_final: 0.8964 (p0)
  outliers start: 19
  outliers final: 16
  residues processed: 79
  average time/residue: 0.0789
  time to fit residues: 9.7829
Evaluate side-chains
  78 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue  280 ILE
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  443 VAL
Chi-restraints excluded: chain D residue  448 THR
Chi-restraints excluded: chain D residue  514 CYS
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  599 THR
Chi-restraints excluded: chain E residue  171 CYS
Chi-restraints excluded: chain E residue  201 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 92 optimal weight:    9.9990
   chunk 132 optimal weight:   40.0000
   chunk 110 optimal weight:    0.9990
   chunk 136 optimal weight:   50.0000
   chunk 61 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 103 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 173 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 = 0.3092 r_free = 0.3092 target = 0.047115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.035913 restraints weight = 76854.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.036946 restraints weight = 41783.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.037658 restraints weight = 27893.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.038063 restraints weight = 21198.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.038443 restraints weight = 17750.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.3387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10961  Z= 0.125
  Angle     :  0.644  19.001  14873  Z= 0.300
  Chirality :  0.039   0.260   1777
  Planarity :  0.003   0.036   1855
  Dihedral  :  3.364  18.728   1480
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 17.43 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.86 (0.24), residues: 1322
  helix:  2.23 (0.18), residues: 849
  sheet: -0.84 (0.55), residues: 88
  loop : -0.50 (0.34), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  90 
 TYR   0.016   0.001   TYR E 121 
 PHE   0.018   0.001   PHE B  64 
 TRP   0.013   0.001   TRP E 131 
 HIS   0.003   0.001   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (10961)
  covalent geometry    : angle       0.64407 (14873)
  hydrogen bonds       : bond        0.03093 (  705)
  hydrogen bonds       : angle       3.81566 ( 2070)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1606.22 seconds
wall clock time: 28 minutes 36.81 seconds (1716.81 seconds total)