Starting phenix.real_space_refine
on Tue Mar  3 21:22:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6p6i_20262/03_2026/6p6i_20262.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6p6i_20262/03_2026/6p6i_20262.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6p6i_20262/03_2026/6p6i_20262.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6p6i_20262/03_2026/6p6i_20262.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6p6i_20262/03_2026/6p6i_20262.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6p6i_20262/03_2026/6p6i_20262.map"
  }
  resolution = 3.67
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      41      5.16       5
     C    5605      2.51       5
     N    1535      2.21       5
     O    1545      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 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: 8726
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4351
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4351
          Classifications: {'peptide': 565}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 24, 'TRANS': 540}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 31
          Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "B"
      Number of atoms: 4375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 568, 4375
          Classifications: {'peptide': 568}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 19, 'TRANS': 548}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 32
  Time building chain proxies: 1.83, per 1000 atoms: 0.21
  Number of scatterers: 8726
  At special positions: 0
  Unit cell: (88.992, 82.944, 132.192, 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      41     16.00
     O    1545      8.00
     N    1535      7.00
     C    5605      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: 0.52
  Conformation dependent library (CDL) restraints added in 284.7 milliseconds
  

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2116

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 5 sheets defined
      68.2% alpha, 3.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 58
      removed outlier: 3.545A  pdb=" N   VAL A  27 " --> pdb=" O   VAL A  23 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   THR A  58 " --> pdb=" O   ASP A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 109
      removed outlier: 3.760A  pdb=" N   LEU A  67 " --> pdb=" O   PRO A  63 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLN A 109 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 115
    Processing helix  chain 'A' and resid 121 through 163
      removed outlier: 5.273A  pdb=" N   VAL A 131 " --> pdb=" O   MET A 127 " (cutoff:3.500A)
      Proline residue:  A 143  - end of helix
      Proline residue:  A 152  - end of helix
      removed outlier: 4.243A  pdb=" N   ILE A 156 " --> pdb=" O   PRO A 152 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   VAL A 157 " --> pdb=" O   LEU A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 184
      removed outlier: 4.358A  pdb=" N   GLY A 177 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   SER A 178 " --> pdb=" O   LEU A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 187
      No H-bonds generated for 'chain 'A' and resid 185 through 187'
    Processing helix  chain 'A' and resid 192 through 206
    Processing helix  chain 'A' and resid 206 through 217
      Proline residue:  A 214  - end of helix
      removed outlier: 3.906A  pdb=" N   ARG A 217 " --> pdb=" O   MET A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 258
      removed outlier: 4.109A  pdb=" N   GLU A 235 " --> pdb=" O   ARG A 231 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   TRP A 236 " --> pdb=" O   ALA A 232 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   ASP A 238 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   THR A 242 " --> pdb=" O   ASP A 238 " (cutoff:3.500A)
      removed outlier: 5.891A  pdb=" N   PHE A 249 " --> pdb=" O   ARG A 245 " (cutoff:3.500A)
      removed outlier: 5.070A  pdb=" N   SER A 250 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 272
      removed outlier: 4.579A  pdb=" N   THR A 263 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 298
      removed outlier: 3.790A  pdb=" N   LEU A 291 " --> pdb=" O   ALA A 287 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   SER A 293 " --> pdb=" O   LEU A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 325
      removed outlier: 3.606A  pdb=" N   GLN A 311 " --> pdb=" O   ASN A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 391
      removed outlier: 4.234A  pdb=" N   ALA A 387 " --> pdb=" O   LYS A 383 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   LEU A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 411
      removed outlier: 3.514A  pdb=" N   ASP A 410 " --> pdb=" O   ASP A 407 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   MET A 411 " --> pdb=" O   LEU A 408 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 407 through 411'
    Processing helix  chain 'A' and resid 414 through 419
    Processing helix  chain 'A' and resid 432 through 439
      removed outlier: 3.572A  pdb=" N   ASN A 437 " --> pdb=" O   THR A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 457
    Processing helix  chain 'A' and resid 459 through 465
      removed outlier: 3.768A  pdb=" N   ILE A 463 " --> pdb=" O   ALA A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 483
    Processing helix  chain 'A' and resid 485 through 497
      removed outlier: 3.643A  pdb=" N   GLN A 497 " --> pdb=" O   ARG A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 525
      removed outlier: 3.986A  pdb=" N   LEU A 519 " --> pdb=" O   ASN A 515 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   ILE A 520 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LYS A 521 " --> pdb=" O   ALA A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 569
    Processing helix  chain 'A' and resid 570 through 582
      removed outlier: 3.551A  pdb=" N   ARG A 574 " --> pdb=" O   GLY A 570 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ALA A 582 " --> pdb=" O   HIS A 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 13 through 22
      removed outlier: 4.482A  pdb=" N   GLN B  18 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 59
      Proline residue:  B  53  - end of helix
    Processing helix  chain 'B' and resid 62 through 93
      removed outlier: 4.137A  pdb=" N   PHE B  90 " --> pdb=" O   TYR B  86 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   GLU B  91 " --> pdb=" O   GLY B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 114
      removed outlier: 4.185A  pdb=" N   GLU B 109 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 121
      removed outlier: 4.108A  pdb=" N   LEU B 119 " --> pdb=" O   PRO B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 136
      removed outlier: 3.605A  pdb=" N   LEU B 132 " --> pdb=" O   ASN B 128 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   GLY B 133 " --> pdb=" O   ALA B 129 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   SER B 134 " --> pdb=" O   LEU B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 164
      removed outlier: 3.861A  pdb=" N   ALA B 146 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   ASN B 147 " --> pdb=" O   ILE B 143 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ILE B 148 " --> pdb=" O   ALA B 144 " (cutoff:3.500A)
      Proline residue:  B 156  - end of helix
    Processing helix  chain 'B' and resid 168 through 178
      removed outlier: 4.067A  pdb=" N   LEU B 172 " --> pdb=" O   TRP B 168 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   VAL B 173 " --> pdb=" O   ARG B 169 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   PHE B 178 " --> pdb=" O   MET B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 216
      Proline residue:  B 190  - end of helix
      removed outlier: 4.280A  pdb=" N   ALA B 202 " --> pdb=" O   THR B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 224
      removed outlier: 3.920A  pdb=" N   GLY B 224 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 260
      removed outlier: 4.584A  pdb=" N   GLN B 250 " --> pdb=" O   ARG B 246 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   LEU B 257 " --> pdb=" O   GLY B 253 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ILE B 258 " --> pdb=" O   ALA B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 280
    Processing helix  chain 'B' and resid 283 through 297
      removed outlier: 3.553A  pdb=" N   MET B 295 " --> pdb=" O   VAL B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 305
      removed outlier: 3.984A  pdb=" N   MET B 301 " --> pdb=" O   PHE B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 325
    Processing helix  chain 'B' and resid 385 through 391
    Processing helix  chain 'B' and resid 413 through 420
    Processing helix  chain 'B' and resid 434 through 439
    Processing helix  chain 'B' and resid 447 through 457
      removed outlier: 3.955A  pdb=" N   ARG B 456 " --> pdb=" O   GLU B 452 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ALA B 457 " --> pdb=" O   GLU B 453 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 467
    Processing helix  chain 'B' and resid 486 through 499
      removed outlier: 3.539A  pdb=" N   ILE B 490 " --> pdb=" O   GLU B 486 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   SER B 491 " --> pdb=" O   ARG B 487 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ALA B 495 " --> pdb=" O   SER B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 528
      removed outlier: 6.900A  pdb=" N   ILE B 514 " --> pdb=" O   ALA B 510 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   GLU B 515 " --> pdb=" O   ALA B 511 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   LEU B 518 " --> pdb=" O   ILE B 514 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   ALA B 519 " --> pdb=" O   GLU B 515 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 544
    Processing helix  chain 'B' and resid 562 through 569
      removed outlier: 3.621A  pdb=" N   LEU B 566 " --> pdb=" O   THR B 562 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 571 through 579
      removed outlier: 4.129A  pdb=" N   ALA B 579 " --> pdb=" O   ALA B 575 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 376
      removed outlier: 3.643A  pdb=" N   LEU A 549 " --> pdb=" O   ALA A 374 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 420 through 423
    Processing sheet with id=AA3, first strand: chain 'B' and resid 364 through 368
      removed outlier: 5.173A  pdb=" N   VAL B 364 " --> pdb=" O   ASN B 348 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   ILE B 344 " --> pdb=" O   PHE B 368 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   SER B 403 " --> pdb=" O   ARG B 345 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ASP B 347 " --> pdb=" O   GLN B 401 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLN B 401 " --> pdb=" O   ASP B 347 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 376 through 377
    Processing sheet with id=AA5, first strand: chain 'B' and resid 421 through 424
      removed outlier: 6.158A  pdb=" N   SER B 422 " --> pdb=" O   ILE B 504 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   ASP B 506 " --> pdb=" O   SER B 422 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   VAL B 424 " --> pdb=" O   ASP B 506 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ILE B 536 " --> pdb=" O   LEU B 505 " (cutoff:3.500A)

    526 hydrogen bonds defined for protein.
    1563 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: 1.34

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2861
        1.34 -     1.46: 1694
        1.46 -     1.58: 4267
        1.58 -     1.70: 0
        1.70 -     1.82: 78
  Bond restraints: 8900
  Sorted by residual:
  bond pdb=" C   ALA B  63 "
       pdb=" N   PRO B  64 "
    ideal  model  delta    sigma   weight residual
    1.336  1.374 -0.038 1.20e-02 6.94e+03 1.01e+01
  bond pdb=" C   THR A 142 "
       pdb=" N   PRO A 143 "
    ideal  model  delta    sigma   weight residual
    1.336  1.372 -0.036 1.23e-02 6.61e+03 8.79e+00
  bond pdb=" N   THR A 433 "
       pdb=" CA  THR A 433 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.29e-02 6.01e+03 7.68e+00
  bond pdb=" C   LEU A 466 "
       pdb=" N   PRO A 467 "
    ideal  model  delta    sigma   weight residual
    1.335  1.362 -0.027 1.30e-02 5.92e+03 4.30e+00
  bond pdb=" C   ARG A 499 "
       pdb=" N   PRO A 500 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 1.38e-02 5.25e+03 3.65e+00
  ... (remaining 8895 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.22: 11416
        2.22 -     4.44: 564
        4.44 -     6.67: 90
        6.67 -     8.89: 33
        8.89 -    11.11: 5
  Bond angle restraints: 12108
  Sorted by residual:
  angle pdb=" N   VAL A 114 "
        pdb=" CA  VAL A 114 "
        pdb=" C   VAL A 114 "
      ideal   model   delta    sigma   weight residual
     112.29  105.44    6.85 9.40e-01 1.13e+00 5.31e+01
  angle pdb=" C   ILE B 166 "
        pdb=" N   ASP B 167 "
        pdb=" CA  ASP B 167 "
      ideal   model   delta    sigma   weight residual
     126.45  135.16   -8.71 1.77e+00 3.19e-01 2.42e+01
  angle pdb=" C   ALA A 148 "
        pdb=" N   ILE A 149 "
        pdb=" CA  ILE A 149 "
      ideal   model   delta    sigma   weight residual
     122.14  116.90    5.24 1.11e+00 8.12e-01 2.23e+01
  angle pdb=" N   LEU B 430 "
        pdb=" CA  LEU B 430 "
        pdb=" C   LEU B 430 "
      ideal   model   delta    sigma   weight residual
     109.95  102.89    7.06 1.59e+00 3.96e-01 1.97e+01
  angle pdb=" C   ASP A 432 "
        pdb=" N   THR A 433 "
        pdb=" CA  THR A 433 "
      ideal   model   delta    sigma   weight residual
     121.54  129.94   -8.40 1.91e+00 2.74e-01 1.93e+01
  ... (remaining 12103 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.41: 4629
       17.41 -    34.82: 534
       34.82 -    52.23: 119
       52.23 -    69.64: 17
       69.64 -    87.05: 15
  Dihedral angle restraints: 5314
    sinusoidal: 2042
      harmonic: 3272
  Sorted by residual:
  dihedral pdb=" CA  ASP B 427 "
           pdb=" C   ASP B 427 "
           pdb=" N   VAL B 428 "
           pdb=" CA  VAL B 428 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.75  -41.25     0      5.00e+00 4.00e-02 6.81e+01
  dihedral pdb=" CA  TRP B 429 "
           pdb=" C   TRP B 429 "
           pdb=" N   LEU B 430 "
           pdb=" CA  LEU B 430 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  139.19   40.81     0      5.00e+00 4.00e-02 6.66e+01
  dihedral pdb=" CA  ALA A 340 "
           pdb=" C   ALA A 340 "
           pdb=" N   SER A 341 "
           pdb=" CA  SER A 341 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.34  -35.66     0      5.00e+00 4.00e-02 5.09e+01
  ... (remaining 5311 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1095
       0.061 -    0.121: 255
       0.121 -    0.182: 60
       0.182 -    0.243: 7
       0.243 -    0.303: 7
  Chirality restraints: 1424
  Sorted by residual:
  chirality pdb=" CB  VAL A  23 "
            pdb=" CA  VAL A  23 "
            pdb=" CG1 VAL A  23 "
            pdb=" CG2 VAL A  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.30e+00
  chirality pdb=" CA  ASP B 167 "
            pdb=" N   ASP B 167 "
            pdb=" C   ASP B 167 "
            pdb=" CB  ASP B 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.97e+00
  chirality pdb=" CA  THR A 142 "
            pdb=" N   THR A 142 "
            pdb=" C   THR A 142 "
            pdb=" CB  THR A 142 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.25    0.27 2.00e-01 2.50e+01 1.85e+00
  ... (remaining 1421 not shown)

  Planarity restraints: 1545
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  21 "    0.051 5.00e-02 4.00e+02   7.60e-02 9.24e+00
        pdb=" N   PRO A  22 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A  22 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A  22 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 413 "   -0.043 5.00e-02 4.00e+02   6.51e-02 6.77e+00
        pdb=" N   PRO B 414 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO B 414 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 414 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 261 "    0.043 5.00e-02 4.00e+02   6.37e-02 6.49e+00
        pdb=" N   PRO A 262 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A 262 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 262 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1542 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1959
        2.78 -     3.31: 8326
        3.31 -     3.84: 14983
        3.84 -     4.37: 16525
        4.37 -     4.90: 28580
  Nonbonded interactions: 70373
  Sorted by model distance:
  nonbonded pdb=" O   GLY B 251 "
            pdb=" OG1 THR B 255 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OE1 GLN A 412 "
            pdb=" OG1 THR A 415 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OG  SER A 384 "
            pdb=" OD1 ASP A 505 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" OG  SER A  88 "
            pdb=" OG1 THR A 142 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" OG1 THR A 343 "
            pdb=" O   ARG A 402 "
     model   vdw
     2.341 3.040
  ... (remaining 70368 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:             2.590
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.570
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.076   8900  Z= 0.310
  Angle     :  1.145  11.110  12108  Z= 0.636
  Chirality :  0.059   0.303   1424
  Planarity :  0.008   0.076   1545
  Dihedral  : 16.150  87.048   3198
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.68 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 12.65 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.46 %

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: -5.14 (0.18), residues: 1129
  helix: -3.13 (0.13), residues: 744
  sheet: -2.34 (0.63), residues: 49
  loop : -3.72 (0.27), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 217 
 TYR   0.017   0.002   TYR B  86 
 PHE   0.025   0.002   PHE A 344 
 TRP   0.026   0.002   TRP A  50 
 HIS   0.011   0.002   HIS B 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00675 ( 8900)
  covalent geometry    : angle       1.14507 (12108)
  hydrogen bonds       : bond        0.12150 (  526)
  hydrogen bonds       : angle       7.25910 ( 1563)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 207
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ARG cc_start: 0.7268 (ttt90) cc_final: 0.6962 (ttt90)
REVERT: A  187 ARG cc_start: 0.6177 (mpt180) cc_final: 0.4255 (ttp-170)
REVERT: A  211 GLN cc_start: 0.7471 (mp10) cc_final: 0.7133 (mm-40)
REVERT: A  297 GLU cc_start: 0.7572 (pp20) cc_final: 0.7315 (pp20)
REVERT: A  521 LYS cc_start: 0.8928 (mtmt) cc_final: 0.8660 (pttp)
REVERT: A  558 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6751 (mm-30)
REVERT: A  559 MET cc_start: 0.7437 (mmm) cc_final: 0.7228 (mmm)
REVERT: B  127 MET cc_start: 0.5692 (mmm) cc_final: 0.5405 (mmm)
REVERT: B  196 MET cc_start: 0.3630 (mmp) cc_final: 0.3340 (mmm)
REVERT: B  217 MET cc_start: 0.4005 (ttm) cc_final: 0.3553 (ttm)
REVERT: B  276 TRP cc_start: 0.6646 (m100) cc_final: 0.6223 (m-10)
REVERT: B  312 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6896 (tp30)
REVERT: B  401 GLN cc_start: 0.8241 (tt0) cc_final: 0.7711 (tt0)
REVERT: B  552 MET cc_start: 0.8047 (mmm) cc_final: 0.7636 (mmm)
REVERT: B  556 GLN cc_start: 0.7921 (mt0) cc_final: 0.7532 (mp10)
  outliers start: 6
  outliers final: 3
  residues processed: 213
  average time/residue: 0.1101
  time to fit residues: 30.8656
Evaluate side-chains
  174 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 171
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue   14 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    0.0370
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    5.9990
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
A  83 GLN
A 230 GLN
A 361 GLN
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 400 HIS
A 458 GLN
B  18 GLN
** B  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 ASN
B 488 GLN
B 521 GLN
B 569 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.173796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.138518 restraints weight = 11257.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.140533 restraints weight = 6990.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.142815 restraints weight = 4843.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.143529 restraints weight = 3579.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.143818 restraints weight = 3586.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7125
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8900  Z= 0.143
  Angle     :  0.712   8.510  12108  Z= 0.362
  Chirality :  0.043   0.181   1424
  Planarity :  0.005   0.066   1545
  Dihedral  :  6.331  39.471   1232
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 17.31 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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: -2.85 (0.22), residues: 1129
  helix: -1.14 (0.17), residues: 739
  sheet: -2.59 (0.59), residues: 63
  loop : -3.25 (0.29), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 440 
 TYR   0.013   0.001   TYR A 272 
 PHE   0.017   0.001   PHE B 297 
 TRP   0.018   0.001   TRP B 429 
 HIS   0.005   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 8900)
  covalent geometry    : angle       0.71217 (12108)
  hydrogen bonds       : bond        0.04465 (  526)
  hydrogen bonds       : angle       5.23337 ( 1563)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 189
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 ARG cc_start: 0.6414 (mpt180) cc_final: 0.4463 (ttp-170)
REVERT: A  201 GLN cc_start: 0.7752 (tm-30) cc_final: 0.7323 (tm-30)
REVERT: A  211 GLN cc_start: 0.7542 (mp10) cc_final: 0.7024 (mp10)
REVERT: A  233 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7241 (mt)
REVERT: A  558 GLU cc_start: 0.6657 (mm-30) cc_final: 0.6353 (mm-30)
  outliers start: 34
  outliers final: 20
  residues processed: 209
  average time/residue: 0.1016
  time to fit residues: 28.5911
Evaluate side-chains
  188 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 167
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  142 VAL
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  409 ILE
Chi-restraints excluded: chain B residue  421 ILE
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  447 THR
Chi-restraints excluded: chain B residue  528 VAL
Chi-restraints excluded: chain B residue  535 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 103 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0970
   chunk 34 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 77 optimal weight:   10.0000
   chunk 71 optimal weight:    0.6980
   chunk 55 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 350 HIS
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 427 ASN
** B  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.174604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.138632 restraints weight = 11334.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.139669 restraints weight = 6514.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.142170 restraints weight = 4438.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.142678 restraints weight = 3724.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.143159 restraints weight = 3303.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8900  Z= 0.142
  Angle     :  0.708   9.068  12108  Z= 0.353
  Chirality :  0.043   0.257   1424
  Planarity :  0.005   0.060   1545
  Dihedral  :  5.802  36.007   1230
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 19.98 %
    Favored  : 75.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: 1129
  helix: -0.27 (0.19), residues: 736
  sheet: -2.27 (0.61), residues: 63
  loop : -3.12 (0.29), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 402 
 TYR   0.014   0.001   TYR B  92 
 PHE   0.016   0.001   PHE B 297 
 TRP   0.018   0.001   TRP B 429 
 HIS   0.004   0.001   HIS B 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 8900)
  covalent geometry    : angle       0.70808 (12108)
  hydrogen bonds       : bond        0.04162 (  526)
  hydrogen bonds       : angle       4.85904 ( 1563)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 185
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 ARG cc_start: 0.6304 (mpt180) cc_final: 0.4607 (ttp-170)
REVERT: A  362 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7878 (mm-30)
REVERT: A  578 HIS cc_start: 0.8649 (m-70) cc_final: 0.8439 (m170)
REVERT: B  415 GLU cc_start: 0.6914 (tp30) cc_final: 0.6646 (tp30)
REVERT: B  447 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8754 (t)
REVERT: B  517 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7431 (mm-30)
REVERT: B  552 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7172 (mmp)
  outliers start: 40
  outliers final: 24
  residues processed: 209
  average time/residue: 0.0973
  time to fit residues: 27.6013
Evaluate side-chains
  198 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 172
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 TRP
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  141 SER
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  142 VAL
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  421 ILE
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  447 THR
Chi-restraints excluded: chain B residue  528 VAL
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  552 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 16 optimal weight:    4.9990
   chunk 23 optimal weight:    0.5980
   chunk 77 optimal weight:    6.9990
   chunk 73 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 100 optimal weight:    0.0980
   chunk 45 optimal weight:    6.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 458 GLN
** B  26 GLN ** 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 = 0.4220 r_free = 0.4220 target = 0.173827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.137997 restraints weight = 11389.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.140382 restraints weight = 6738.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.142537 restraints weight = 4527.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.142907 restraints weight = 3427.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.143089 restraints weight = 3619.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8900  Z= 0.143
  Angle     :  0.692   9.749  12108  Z= 0.345
  Chirality :  0.043   0.235   1424
  Planarity :  0.005   0.057   1545
  Dihedral  :  5.597  35.306   1230
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 21.09 %
    Favored  : 74.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -1.35 (0.25), residues: 1129
  helix:  0.15 (0.19), residues: 737
  sheet: -2.22 (0.60), residues: 63
  loop : -2.97 (0.30), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 296 
 TYR   0.015   0.001   TYR B  92 
 PHE   0.020   0.001   PHE B 297 
 TRP   0.019   0.001   TRP B 429 
 HIS   0.004   0.001   HIS B 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8900)
  covalent geometry    : angle       0.69219 (12108)
  hydrogen bonds       : bond        0.04046 (  526)
  hydrogen bonds       : angle       4.66586 ( 1563)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 181
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 ARG cc_start: 0.6172 (mpt180) cc_final: 0.4528 (ttp-170)
REVERT: A  362 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7774 (mm-30)
REVERT: A  498 ASP cc_start: 0.7621 (t0) cc_final: 0.7244 (t0)
REVERT: B  348 ASN cc_start: 0.7548 (t0) cc_final: 0.7284 (t0)
REVERT: B  415 GLU cc_start: 0.6907 (tp30) cc_final: 0.6615 (tp30)
REVERT: B  447 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8686 (t)
REVERT: B  517 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7101 (mm-30)
  outliers start: 38
  outliers final: 31
  residues processed: 206
  average time/residue: 0.0996
  time to fit residues: 27.8072
Evaluate side-chains
  202 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 170
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   50 TRP
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   52 TYR
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 VAL
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  421 ILE
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  447 THR
Chi-restraints excluded: chain B residue  490 ILE
Chi-restraints excluded: chain B residue  528 VAL
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  563 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 88 optimal weight:    7.9990
   chunk 36 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 80 optimal weight:    4.9990
   chunk 39 optimal weight:    6.9990
   chunk 93 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0980
   chunk 3 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
A 135 HIS
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 578 HIS
** B  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.167717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.130661 restraints weight = 11666.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.132868 restraints weight = 7517.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.135212 restraints weight = 5007.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.135586 restraints weight = 3736.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.135808 restraints weight = 3785.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8900  Z= 0.241
  Angle     :  0.811   9.832  12108  Z= 0.400
  Chirality :  0.047   0.275   1424
  Planarity :  0.005   0.056   1545
  Dihedral  :  5.957  37.781   1230
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 14.87
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.15 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 21.75 %
    Favored  : 73.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -1.45 (0.25), residues: 1129
  helix:  0.00 (0.19), residues: 739
  sheet: -2.37 (0.58), residues: 63
  loop : -2.79 (0.31), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 296 
 TYR   0.017   0.002   TYR B  92 
 PHE   0.018   0.002   PHE B 297 
 TRP   0.022   0.002   TRP B 429 
 HIS   0.005   0.001   HIS A 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00549 ( 8900)
  covalent geometry    : angle       0.81067 (12108)
  hydrogen bonds       : bond        0.04774 (  526)
  hydrogen bonds       : angle       5.00087 ( 1563)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 178
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 ARG cc_start: 0.6182 (mpt180) cc_final: 0.4595 (ttp-170)
REVERT: A  213 MET cc_start: 0.8211 (mmm) cc_final: 0.7917 (mmm)
REVERT: B  185 TYR cc_start: 0.8003 (t80) cc_final: 0.7640 (t80)
REVERT: B  296 ARG cc_start: 0.8053 (mmm160) cc_final: 0.7699 (mmm160)
REVERT: B  415 GLU cc_start: 0.6848 (tp30) cc_final: 0.6637 (tp30)
REVERT: B  489 ARG cc_start: 0.7389 (mtm-85) cc_final: 0.7165 (mtm-85)
REVERT: B  552 MET cc_start: 0.7416 (mmp) cc_final: 0.7103 (mmp)
REVERT: B  563 HIS cc_start: 0.7160 (OUTLIER) cc_final: 0.6417 (p-80)
  outliers start: 46
  outliers final: 32
  residues processed: 208
  average time/residue: 0.1028
  time to fit residues: 28.7941
Evaluate side-chains
  201 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 168
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   50 TRP
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  562 HIS
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 VAL
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain B residue  473 THR
Chi-restraints excluded: chain B residue  490 ILE
Chi-restraints excluded: chain B residue  528 VAL
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  563 HIS
Chi-restraints excluded: chain B residue  572 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 81 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 63 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   chunk 75 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  26 GLN ** 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 = 0.4196 r_free = 0.4196 target = 0.171457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.135150 restraints weight = 11452.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.137629 restraints weight = 6878.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.140028 restraints weight = 4533.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.140386 restraints weight = 3445.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.141440 restraints weight = 3573.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7159
moved from start:          0.3122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8900  Z= 0.159
  Angle     :  0.750  10.628  12108  Z= 0.364
  Chirality :  0.044   0.263   1424
  Planarity :  0.004   0.053   1545
  Dihedral  :  5.683  35.864   1230
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 23.64 %
    Favored  : 71.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -1.09 (0.25), residues: 1129
  helix:  0.30 (0.20), residues: 737
  sheet: -2.35 (0.59), residues: 63
  loop : -2.67 (0.32), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 296 
 TYR   0.016   0.001   TYR B  92 
 PHE   0.015   0.001   PHE B 297 
 TRP   0.019   0.001   TRP B 429 
 HIS   0.007   0.001   HIS B  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 8900)
  covalent geometry    : angle       0.75001 (12108)
  hydrogen bonds       : bond        0.04252 (  526)
  hydrogen bonds       : angle       4.74640 ( 1563)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 173
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 ARG cc_start: 0.6132 (mpt180) cc_final: 0.4574 (ttp-170)
REVERT: A  213 MET cc_start: 0.8153 (mmm) cc_final: 0.7863 (mmm)
REVERT: A  424 PHE cc_start: 0.7096 (m-80) cc_final: 0.6876 (m-10)
REVERT: B  296 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7649 (mmm160)
REVERT: B  489 ARG cc_start: 0.7327 (mtm-85) cc_final: 0.7071 (mtm-85)
REVERT: B  563 HIS cc_start: 0.7151 (OUTLIER) cc_final: 0.6379 (p-80)
  outliers start: 48
  outliers final: 36
  residues processed: 207
  average time/residue: 0.0931
  time to fit residues: 26.5372
Evaluate side-chains
  205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 168
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   50 TRP
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  562 HIS
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 VAL
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  413 THR
Chi-restraints excluded: chain B residue  421 ILE
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain B residue  473 THR
Chi-restraints excluded: chain B residue  490 ILE
Chi-restraints excluded: chain B residue  528 VAL
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  563 HIS
Chi-restraints excluded: chain B residue  572 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 42 optimal weight:    9.9990
   chunk 45 optimal weight:    6.9990
   chunk 99 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   chunk 85 optimal weight:    0.0010
   chunk 32 optimal weight:    0.3980
   chunk 37 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 65 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 346 GLN
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  26 GLN ** 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 = 0.4225 r_free = 0.4225 target = 0.174064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.139086 restraints weight = 11445.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.141328 restraints weight = 7274.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.143736 restraints weight = 4748.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.144055 restraints weight = 3576.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.144507 restraints weight = 3467.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.3344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8900  Z= 0.139
  Angle     :  0.742  11.446  12108  Z= 0.358
  Chirality :  0.044   0.282   1424
  Planarity :  0.004   0.049   1545
  Dihedral  :  5.445  34.105   1230
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.88 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 24.75 %
    Favored  : 70.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.85 (0.25), residues: 1129
  helix:  0.50 (0.20), residues: 737
  sheet: -2.39 (0.59), residues: 65
  loop : -2.56 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 296 
 TYR   0.016   0.001   TYR B  92 
 PHE   0.013   0.001   PHE B 237 
 TRP   0.018   0.001   TRP B 429 
 HIS   0.005   0.001   HIS B 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8900)
  covalent geometry    : angle       0.74209 (12108)
  hydrogen bonds       : bond        0.04029 (  526)
  hydrogen bonds       : angle       4.58361 ( 1563)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 175
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 ILE cc_start: 0.8112 (mm) cc_final: 0.7845 (mt)
REVERT: A  187 ARG cc_start: 0.6035 (mpt180) cc_final: 0.4504 (ttp-170)
REVERT: A  213 MET cc_start: 0.8053 (mmm) cc_final: 0.7808 (mmm)
REVERT: A  424 PHE cc_start: 0.7060 (m-80) cc_final: 0.6816 (m-10)
REVERT: A  498 ASP cc_start: 0.7558 (t0) cc_final: 0.7224 (t0)
REVERT: A  550 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8938 (tt)
REVERT: B  348 ASN cc_start: 0.7522 (t0) cc_final: 0.7287 (t0)
REVERT: B  563 HIS cc_start: 0.7104 (OUTLIER) cc_final: 0.6275 (p90)
  outliers start: 40
  outliers final: 35
  residues processed: 206
  average time/residue: 0.0944
  time to fit residues: 26.5227
Evaluate side-chains
  206 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 169
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   50 TRP
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  562 HIS
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 VAL
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  413 THR
Chi-restraints excluded: chain B residue  421 ILE
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain B residue  473 THR
Chi-restraints excluded: chain B residue  490 ILE
Chi-restraints excluded: chain B residue  528 VAL
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  563 HIS
Chi-restraints excluded: chain B residue  572 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 83 optimal weight:    0.3980
   chunk 40 optimal weight:    0.6980
   chunk 88 optimal weight:    0.2980
   chunk 22 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 215 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.174063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.138903 restraints weight = 11393.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.140975 restraints weight = 7155.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.143185 restraints weight = 4876.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.143861 restraints weight = 3591.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.144158 restraints weight = 3444.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.3496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8900  Z= 0.141
  Angle     :  0.745  11.509  12108  Z= 0.360
  Chirality :  0.043   0.260   1424
  Planarity :  0.004   0.048   1545
  Dihedral  :  5.358  33.191   1230
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 25.08 %
    Favored  : 70.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.63 (0.26), residues: 1129
  helix:  0.63 (0.20), residues: 745
  sheet: -2.21 (0.61), residues: 64
  loop : -2.50 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 296 
 TYR   0.016   0.001   TYR B  92 
 PHE   0.016   0.001   PHE B 237 
 TRP   0.017   0.001   TRP B 429 
 HIS   0.005   0.001   HIS B 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8900)
  covalent geometry    : angle       0.74546 (12108)
  hydrogen bonds       : bond        0.04012 (  526)
  hydrogen bonds       : angle       4.49377 ( 1563)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 176
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 ARG cc_start: 0.5902 (mpt180) cc_final: 0.4458 (ttp-170)
REVERT: A  213 MET cc_start: 0.8115 (mmm) cc_final: 0.7889 (mmm)
REVERT: A  375 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7780 (pp)
REVERT: A  498 ASP cc_start: 0.7479 (t0) cc_final: 0.7229 (t0)
REVERT: A  550 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8644 (tt)
REVERT: A  565 LEU cc_start: 0.7939 (mp) cc_final: 0.7599 (mp)
REVERT: B  217 MET cc_start: 0.3552 (tpp) cc_final: 0.2385 (tpp)
REVERT: B  348 ASN cc_start: 0.7507 (t0) cc_final: 0.7280 (t0)
REVERT: B  552 MET cc_start: 0.6932 (mmp) cc_final: 0.6614 (mmp)
REVERT: B  563 HIS cc_start: 0.7048 (OUTLIER) cc_final: 0.6259 (p-80)
  outliers start: 42
  outliers final: 36
  residues processed: 209
  average time/residue: 0.0923
  time to fit residues: 26.4050
Evaluate side-chains
  210 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 171
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   50 TRP
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  426 ASP
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  562 HIS
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 VAL
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  421 ILE
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  473 THR
Chi-restraints excluded: chain B residue  490 ILE
Chi-restraints excluded: chain B residue  528 VAL
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  563 HIS
Chi-restraints excluded: chain B residue  572 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 34 optimal weight:    9.9990
   chunk 65 optimal weight:    0.9990
   chunk 76 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 497 GLN ** 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 = 0.4218 r_free = 0.4218 target = 0.173118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.137581 restraints weight = 11304.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.139930 restraints weight = 7164.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.142104 restraints weight = 4946.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.142479 restraints weight = 3643.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.143412 restraints weight = 3749.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.3593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8900  Z= 0.159
  Angle     :  0.775  16.336  12108  Z= 0.374
  Chirality :  0.044   0.293   1424
  Planarity :  0.004   0.048   1545
  Dihedral  :  5.436  33.644   1230
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 24.86 %
    Favored  : 70.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.67 (0.26), residues: 1129
  helix:  0.60 (0.20), residues: 747
  sheet: -2.12 (0.61), residues: 62
  loop : -2.54 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 246 
 TYR   0.015   0.001   TYR B  92 
 PHE   0.020   0.001   PHE B 213 
 TRP   0.018   0.001   TRP B 429 
 HIS   0.004   0.001   HIS B 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 8900)
  covalent geometry    : angle       0.77496 (12108)
  hydrogen bonds       : bond        0.04121 (  526)
  hydrogen bonds       : angle       4.54629 ( 1563)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 171
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 ARG cc_start: 0.5903 (mpt180) cc_final: 0.4517 (ttp-170)
REVERT: A  498 ASP cc_start: 0.7463 (t0) cc_final: 0.7234 (t0)
REVERT: B  348 ASN cc_start: 0.7516 (t0) cc_final: 0.6851 (t0)
REVERT: B  399 GLN cc_start: 0.7533 (tm-30) cc_final: 0.7233 (tm-30)
REVERT: B  552 MET cc_start: 0.7056 (mmp) cc_final: 0.6732 (mmp)
REVERT: B  563 HIS cc_start: 0.7028 (OUTLIER) cc_final: 0.6220 (p-80)
  outliers start: 44
  outliers final: 37
  residues processed: 206
  average time/residue: 0.0938
  time to fit residues: 26.5041
Evaluate side-chains
  205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 167
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   50 TRP
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  426 ASP
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 VAL
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  413 THR
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  447 THR
Chi-restraints excluded: chain B residue  473 THR
Chi-restraints excluded: chain B residue  490 ILE
Chi-restraints excluded: chain B residue  528 VAL
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  563 HIS
Chi-restraints excluded: chain B residue  572 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 90 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   chunk 72 optimal weight:    0.5980
   chunk 81 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  95 HIS ** 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 = 0.4221 r_free = 0.4221 target = 0.173466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.138606 restraints weight = 11372.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.139194 restraints weight = 7630.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.140803 restraints weight = 5444.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.141091 restraints weight = 4306.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.143915 restraints weight = 3930.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7129
moved from start:          0.3665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8900  Z= 0.154
  Angle     :  0.794  16.307  12108  Z= 0.381
  Chirality :  0.045   0.305   1424
  Planarity :  0.005   0.048   1545
  Dihedral  :  5.430  33.046   1230
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 25.19 %
    Favored  : 70.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.67 (0.26), residues: 1129
  helix:  0.63 (0.20), residues: 746
  sheet: -2.28 (0.60), residues: 64
  loop : -2.57 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 246 
 TYR   0.016   0.001   TYR B  92 
 PHE   0.014   0.001   PHE B 213 
 TRP   0.018   0.001   TRP B 429 
 HIS   0.004   0.001   HIS B 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 8900)
  covalent geometry    : angle       0.79383 (12108)
  hydrogen bonds       : bond        0.04072 (  526)
  hydrogen bonds       : angle       4.59962 ( 1563)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 166
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 HIS cc_start: 0.6113 (OUTLIER) cc_final: 0.5744 (t70)
REVERT: A  187 ARG cc_start: 0.5871 (mpt180) cc_final: 0.4516 (ttp-170)
REVERT: A  498 ASP cc_start: 0.7422 (t0) cc_final: 0.7206 (t0)
REVERT: B  348 ASN cc_start: 0.7544 (t0) cc_final: 0.6895 (t0)
REVERT: B  399 GLN cc_start: 0.7552 (tm-30) cc_final: 0.7258 (tm-30)
REVERT: B  552 MET cc_start: 0.7072 (mmp) cc_final: 0.6727 (mmp)
REVERT: B  563 HIS cc_start: 0.7048 (OUTLIER) cc_final: 0.6229 (p-80)
  outliers start: 43
  outliers final: 38
  residues processed: 200
  average time/residue: 0.0933
  time to fit residues: 25.6995
Evaluate side-chains
  204 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 164
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   50 TRP
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  426 ASP
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 VAL
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  413 THR
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  447 THR
Chi-restraints excluded: chain B residue  473 THR
Chi-restraints excluded: chain B residue  490 ILE
Chi-restraints excluded: chain B residue  528 VAL
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  563 HIS
Chi-restraints excluded: chain B residue  572 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 95 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 111 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0270
   chunk 75 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  95 HIS ** 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 = 0.4220 r_free = 0.4220 target = 0.172238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.136843 restraints weight = 11321.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.136925 restraints weight = 7412.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.139001 restraints weight = 5226.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.140524 restraints weight = 3985.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.140555 restraints weight = 3589.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7157
moved from start:          0.3759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8900  Z= 0.150
  Angle     :  0.794  18.609  12108  Z= 0.379
  Chirality :  0.045   0.328   1424
  Planarity :  0.005   0.053   1545
  Dihedral  :  5.370  32.685   1230
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 26.19 %
    Favored  : 69.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.60 (0.26), residues: 1129
  helix:  0.67 (0.20), residues: 746
  sheet: -2.26 (0.60), residues: 64
  loop : -2.52 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG B 221 
 TYR   0.020   0.001   TYR A 579 
 PHE   0.014   0.001   PHE B 237 
 TRP   0.018   0.001   TRP B 429 
 HIS   0.004   0.001   HIS B 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 8900)
  covalent geometry    : angle       0.79423 (12108)
  hydrogen bonds       : bond        0.04058 (  526)
  hydrogen bonds       : angle       4.59593 ( 1563)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1492.91 seconds
wall clock time: 26 minutes 24.68 seconds (1584.68 seconds total)