Starting phenix.real_space_refine
on Thu Feb 13 07:26:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6p6i_20262/02_2025/6p6i_20262.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6p6i_20262/02_2025/6p6i_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6p6i_20262/02_2025/6p6i_20262.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6p6i_20262/02_2025/6p6i_20262.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6p6i_20262/02_2025/6p6i_20262.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6p6i_20262/02_2025/6p6i_20262.cif"
  }
  resolution = 3.67
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLU:plan': 1, 'ARG:plan': 5}
          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: 5.95, per 1000 atoms: 0.68
  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: 2.25
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.88
  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: 2.47

  Time building geometry restraints manager: 2.59 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:             1.950
  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:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.380
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.910
-------------------------------------------------------------------------------
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= 0.444
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.026   0.002   TRP A  50 
 HIS   0.011   0.002   HIS B 248 
 PHE   0.025   0.002   PHE A 344 
 TYR   0.017   0.002   TYR B  86 
 ARG   0.008   0.001   ARG A 217 

*********************** 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  : 1.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ARG cc_start: 0.7268 (ttt90) cc_final: 0.6960 (ttt90)
REVERT: A  187 ARG cc_start: 0.6178 (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: 0.7227 (mmm)
REVERT: B  127 MET cc_start: 0.5692 (mmm) cc_final: 0.5404 (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: 0.3551 (ttm)
REVERT: B  276 TRP cc_start: 0.6646 (m100) cc_final: 0.6224 (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: 0.7531 (mp10)
  outliers start: 6
  outliers final: 3
  residues processed: 213
  average time/residue: 0.2710
  time to fit residues: 75.6917
Evaluate side-chains
  173 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 170
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
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 94 optimal weight:    0.9980
   chunk 84 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 57 optimal weight:    0.1980
   chunk 45 optimal weight:    3.9990
   chunk 87 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   chunk 65 optimal weight:    0.5980
   chunk 101 optimal weight:    0.9980
   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  83 GLN
A 230 GLN
A 361 GLN
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 400 HIS
A 427 ASN
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 530 ASN
B 569 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.174237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.138037 restraints weight = 11140.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.140673 restraints weight = 6419.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.142691 restraints weight = 4331.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.1859

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= 0.196
  Angle     :  0.704   8.452  12108  Z= 0.357
  Chirality :  0.043   0.176   1424
  Planarity :  0.005   0.065   1545
  Dihedral  :  6.234  38.836   1232
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 17.76 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.77 (0.22), residues: 1129
  helix: -1.08 (0.17), residues: 740
  sheet: -2.55 (0.60), residues: 63
  loop : -3.23 (0.30), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 429 
 HIS   0.005   0.001   HIS A 578 
 PHE   0.017   0.001   PHE B 297 
 TYR   0.013   0.001   TYR A 272 
 ARG   0.007   0.000   ARG B 440 

*********************** 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
  229 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 192
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 ARG cc_start: 0.6359 (mpt180) cc_final: 0.4397 (ttp-170)
REVERT: A  201 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7487 (tm-30)
REVERT: A  211 GLN cc_start: 0.7515 (mp10) cc_final: 0.7017 (mp10)
REVERT: A  233 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7244 (mt)
REVERT: A  311 GLN cc_start: 0.8025 (pp30) cc_final: 0.7622 (pp30)
REVERT: A  558 GLU cc_start: 0.6699 (mm-30) cc_final: 0.6393 (mm-30)
REVERT: B  323 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7774 (pp30)
  outliers start: 37
  outliers final: 21
  residues processed: 214
  average time/residue: 0.2447
  time to fit residues: 69.9703
Evaluate side-chains
  192 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 170
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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   71 MET
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 5 optimal weight:    0.1980
   chunk 60 optimal weight:    0.5980
   chunk 56 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 85 optimal weight:    0.6980
   chunk 63 optimal weight:    0.5980
   chunk 83 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   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 350 HIS
** A 371 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 = 0.174596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.137986 restraints weight = 11295.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.140624 restraints weight = 6611.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.142710 restraints weight = 4444.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7135
moved from start:          0.2512

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= 0.201
  Angle     :  0.704   9.271  12108  Z= 0.351
  Chirality :  0.043   0.247   1424
  Planarity :  0.005   0.060   1545
  Dihedral  :  5.765  35.782   1230
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.88 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 20.20 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.85 (0.24), residues: 1129
  helix: -0.25 (0.19), residues: 736
  sheet: -2.23 (0.61), residues: 63
  loop : -3.15 (0.29), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 429 
 HIS   0.004   0.001   HIS B 563 
 PHE   0.019   0.001   PHE B 297 
 TYR   0.014   0.001   TYR B  92 
 ARG   0.006   0.000   ARG B 296 

*********************** 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  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 ARG cc_start: 0.6269 (mpt180) cc_final: 0.4593 (ttp-170)
REVERT: A  362 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7816 (mm-30)
REVERT: A  574 ARG cc_start: 0.7498 (tmt170) cc_final: 0.6988 (tmt170)
REVERT: B  323 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7823 (pp30)
REVERT: B  415 GLU cc_start: 0.6850 (tp30) cc_final: 0.6599 (tp30)
REVERT: B  447 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8711 (t)
REVERT: B  517 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7227 (mm-30)
REVERT: B  552 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7238 (mmp)
  outliers start: 40
  outliers final: 27
  residues processed: 209
  average time/residue: 0.2490
  time to fit residues: 69.0068
Evaluate side-chains
  200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 171
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
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  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  406 VAL
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   71 MET
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
Chi-restraints excluded: chain B residue  572 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 88 optimal weight:    8.9990
   chunk 26 optimal weight:    0.5980
   chunk 108 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 77 optimal weight:    8.9990
   chunk 62 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 81 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 578 HIS
** 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 = 0.4206 r_free = 0.4206 target = 0.172417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.136612 restraints weight = 11332.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.138850 restraints weight = 7294.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.140972 restraints weight = 5055.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.2843

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= 0.233
  Angle     :  0.707   9.565  12108  Z= 0.353
  Chirality :  0.044   0.240   1424
  Planarity :  0.005   0.058   1545
  Dihedral  :  5.675  35.958   1230
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 22.09 %
    Favored  : 73.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.25), residues: 1129
  helix:  0.10 (0.19), residues: 735
  sheet: -2.19 (0.61), residues: 63
  loop : -2.98 (0.30), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 429 
 HIS   0.007   0.001   HIS A 578 
 PHE   0.016   0.001   PHE B 297 
 TYR   0.015   0.002   TYR B  92 
 ARG   0.005   0.000   ARG A 402 

*********************** 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
  221 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 179
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 ARG cc_start: 0.6082 (mpt180) cc_final: 0.4484 (ttp-170)
REVERT: A  197 LYS cc_start: 0.8200 (tmmt) cc_final: 0.7699 (tptp)
REVERT: A  362 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7770 (mm-30)
REVERT: B  185 TYR cc_start: 0.7882 (t80) cc_final: 0.7406 (t80)
REVERT: B  296 ARG cc_start: 0.7898 (mmm160) cc_final: 0.7633 (mmm160)
REVERT: B  323 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7835 (pp30)
REVERT: B  348 ASN cc_start: 0.7509 (t0) cc_final: 0.7227 (t0)
REVERT: B  415 GLU cc_start: 0.6855 (tp30) cc_final: 0.6597 (tp30)
REVERT: B  447 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8647 (t)
REVERT: B  517 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7261 (mm-30)
REVERT: B  563 HIS cc_start: 0.7092 (OUTLIER) cc_final: 0.6377 (p-80)
  outliers start: 42
  outliers final: 29
  residues processed: 205
  average time/residue: 0.2438
  time to fit residues: 66.2235
Evaluate side-chains
  202 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 171
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
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  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 A residue  562 HIS
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  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 83 optimal weight:    0.1980
   chunk 29 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 100 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 55 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9980
   chunk 85 optimal weight:    0.4980
   chunk 104 optimal weight:    0.6980
   chunk 90 optimal weight:    0.0970
   overall best weight:    0.4378

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.175781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.140369 restraints weight = 11271.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.143496 restraints weight = 6683.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.144881 restraints weight = 4256.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7088
moved from start:          0.3172

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= 0.184
  Angle     :  0.685  10.351  12108  Z= 0.337
  Chirality :  0.043   0.265   1424
  Planarity :  0.004   0.052   1545
  Dihedral  :  5.383  34.352   1230
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 22.53 %
    Favored  : 73.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.25), residues: 1129
  helix:  0.44 (0.20), residues: 737
  sheet: -2.30 (0.59), residues: 65
  loop : -2.74 (0.31), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 429 
 HIS   0.004   0.001   HIS B 248 
 PHE   0.017   0.001   PHE B 297 
 TYR   0.014   0.001   TYR B  92 
 ARG   0.005   0.000   ARG B 345 

*********************** 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
  223 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 183
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 HIS cc_start: 0.6013 (OUTLIER) cc_final: 0.5730 (t-170)
REVERT: A  187 ARG cc_start: 0.6082 (mpt180) cc_final: 0.4478 (ttp-170)
REVERT: A  362 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7765 (mm-30)
REVERT: A  424 PHE cc_start: 0.7307 (m-80) cc_final: 0.7083 (m-80)
REVERT: A  498 ASP cc_start: 0.7591 (t0) cc_final: 0.7235 (t0)
REVERT: B  132 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7553 (mt)
REVERT: B  185 TYR cc_start: 0.7755 (t80) cc_final: 0.7478 (t80)
REVERT: B  323 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7872 (pp30)
REVERT: B  348 ASN cc_start: 0.7508 (t0) cc_final: 0.7230 (t0)
REVERT: B  552 MET cc_start: 0.7230 (mmp) cc_final: 0.6935 (mmp)
REVERT: B  563 HIS cc_start: 0.7165 (OUTLIER) cc_final: 0.6442 (p90)
  outliers start: 40
  outliers final: 26
  residues processed: 209
  average time/residue: 0.2269
  time to fit residues: 63.8563
Evaluate side-chains
  201 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 172
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
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  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  305 LEU
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  519 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue   52 TYR
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  132 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  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  472 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 86 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 105 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   chunk 106 optimal weight:    0.0070
   chunk 65 optimal weight:    0.6980
   chunk 110 optimal weight:    0.2980
   chunk 26 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   overall best weight:    0.4198

-------------------------------------------------------------------------------
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 242 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.176100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.141573 restraints weight = 11203.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.143109 restraints weight = 7051.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.145304 restraints weight = 4983.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7082
moved from start:          0.3376

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= 0.188
  Angle     :  0.692  10.989  12108  Z= 0.339
  Chirality :  0.042   0.244   1424
  Planarity :  0.004   0.049   1545
  Dihedral  :  5.270  33.251   1230
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 23.42 %
    Favored  : 72.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.25), residues: 1129
  helix:  0.65 (0.20), residues: 735
  sheet: -2.21 (0.59), residues: 65
  loop : -2.73 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 429 
 HIS   0.004   0.001   HIS B 248 
 PHE   0.017   0.001   PHE B 297 
 TYR   0.014   0.001   TYR B  92 
 ARG   0.004   0.000   ARG B 345 

*********************** 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
  217 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 177
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 HIS cc_start: 0.5993 (OUTLIER) cc_final: 0.5709 (t-170)
REVERT: A  187 ARG cc_start: 0.5973 (mpt180) cc_final: 0.4455 (ttp-170)
REVERT: A  362 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7787 (mm-30)
REVERT: A  424 PHE cc_start: 0.7334 (m-80) cc_final: 0.7023 (m-80)
REVERT: A  498 ASP cc_start: 0.7449 (t0) cc_final: 0.7148 (t0)
REVERT: A  559 MET cc_start: 0.6562 (mmm) cc_final: 0.6297 (mmm)
REVERT: B  323 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7864 (pp30)
REVERT: B  348 ASN cc_start: 0.7453 (t0) cc_final: 0.7204 (t0)
REVERT: B  447 THR cc_start: 0.8885 (p) cc_final: 0.8679 (t)
REVERT: B  563 HIS cc_start: 0.7105 (OUTLIER) cc_final: 0.6383 (p90)
  outliers start: 40
  outliers final: 30
  residues processed: 205
  average time/residue: 0.2300
  time to fit residues: 64.1184
Evaluate side-chains
  204 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 172
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
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  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  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  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   81 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  132 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  222 THR
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  430 LEU
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 101 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 111 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 67 optimal weight:    7.9990
   chunk 84 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.4201 r_free = 0.4201 target = 0.171148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.134220 restraints weight = 11422.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.136364 restraints weight = 7052.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.138460 restraints weight = 4865.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
moved from start:          0.3305

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= 0.277
  Angle     :  0.761  11.119  12108  Z= 0.371
  Chirality :  0.045   0.266   1424
  Planarity :  0.004   0.048   1545
  Dihedral  :  5.537  34.946   1230
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 24.08 %
    Favored  : 70.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.25), residues: 1129
  helix:  0.56 (0.20), residues: 741
  sheet: -2.20 (0.60), residues: 65
  loop : -2.67 (0.32), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 429 
 HIS   0.004   0.001   HIS A 135 
 PHE   0.018   0.002   PHE B 297 
 TYR   0.015   0.002   TYR B  92 
 ARG   0.006   0.000   ARG B 296 

*********************** 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
  222 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 177
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 HIS cc_start: 0.6219 (OUTLIER) cc_final: 0.5957 (t-90)
REVERT: A  187 ARG cc_start: 0.5923 (mpt180) cc_final: 0.4463 (ttp-170)
REVERT: A  398 LYS cc_start: 0.8577 (tptp) cc_final: 0.8344 (ptpp)
REVERT: A  424 PHE cc_start: 0.7475 (m-80) cc_final: 0.7120 (m-80)
REVERT: A  498 ASP cc_start: 0.7579 (t0) cc_final: 0.7251 (t0)
REVERT: B  185 TYR cc_start: 0.7860 (t80) cc_final: 0.7618 (t80)
REVERT: B  323 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7900 (pp30)
REVERT: B  348 ASN cc_start: 0.7557 (t0) cc_final: 0.7229 (t0)
REVERT: B  447 THR cc_start: 0.9003 (p) cc_final: 0.8709 (t)
REVERT: B  552 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.7011 (mmp)
REVERT: B  563 HIS cc_start: 0.7055 (OUTLIER) cc_final: 0.6266 (p-80)
  outliers start: 45
  outliers final: 30
  residues processed: 212
  average time/residue: 0.2356
  time to fit residues: 66.5451
Evaluate side-chains
  203 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 170
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
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  135 HIS
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  211 GLN
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 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  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  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  552 MET
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 107 optimal weight:    4.9990
   chunk 42 optimal weight:   10.0000
   chunk 34 optimal weight:    8.9990
   chunk 38 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   chunk 103 optimal weight:    0.2980
   chunk 23 optimal weight:    0.6980
   chunk 95 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    1.5986

-------------------------------------------------------------------------------
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  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 = 0.4166 r_free = 0.4166 target = 0.167607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.130174 restraints weight = 11578.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.131767 restraints weight = 7141.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.133844 restraints weight = 4799.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.3251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   8900  Z= 0.361
  Angle     :  0.829  11.788  12108  Z= 0.408
  Chirality :  0.049   0.285   1424
  Planarity :  0.005   0.049   1545
  Dihedral  :  5.906  36.505   1230
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 15.33
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.41 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 26.19 %
    Favored  : 69.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.25), residues: 1129
  helix:  0.33 (0.19), residues: 735
  sheet: -2.11 (0.61), residues: 63
  loop : -2.53 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 429 
 HIS   0.005   0.001   HIS A 135 
 PHE   0.018   0.002   PHE B 237 
 TYR   0.017   0.002   TYR B  92 
 ARG   0.011   0.001   ARG B 296 

*********************** 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
  213 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 173
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 HIS cc_start: 0.6376 (OUTLIER) cc_final: 0.6130 (t-90)
REVERT: A  187 ARG cc_start: 0.6043 (mpt180) cc_final: 0.4550 (ttp-170)
REVERT: A  295 MET cc_start: 0.7891 (tmm) cc_final: 0.7393 (tmm)
REVERT: A  362 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7908 (mm-30)
REVERT: A  498 ASP cc_start: 0.7675 (t0) cc_final: 0.7289 (t0)
REVERT: A  559 MET cc_start: 0.6984 (mmm) cc_final: 0.6745 (mmm)
REVERT: B  323 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7883 (pp30)
REVERT: B  447 THR cc_start: 0.9072 (p) cc_final: 0.8810 (t)
REVERT: B  563 HIS cc_start: 0.7127 (OUTLIER) cc_final: 0.6323 (p-80)
  outliers start: 40
  outliers final: 32
  residues processed: 204
  average time/residue: 0.2408
  time to fit residues: 65.4498
Evaluate side-chains
  202 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 168
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
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  135 HIS
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  211 GLN
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  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  142 VAL
Chi-restraints excluded: chain B residue  164 LEU
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  385 THR
Chi-restraints excluded: chain B residue  413 THR
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  552 MET
Chi-restraints excluded: chain B residue  563 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   chunk 84 optimal weight:    0.5980
   chunk 50 optimal weight:    4.9990
   chunk 109 optimal weight:    0.5980
   chunk 101 optimal weight:    0.2980
   chunk 64 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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**

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 = 0.173104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.137130 restraints weight = 11403.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.139412 restraints weight = 6668.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.141457 restraints weight = 4418.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.3464

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= 0.215
  Angle     :  0.769  12.176  12108  Z= 0.371
  Chirality :  0.045   0.303   1424
  Planarity :  0.004   0.049   1545
  Dihedral  :  5.531  34.214   1230
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 26.86 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.25), residues: 1129
  helix:  0.57 (0.20), residues: 737
  sheet: -2.23 (0.60), residues: 65
  loop : -2.55 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 429 
 HIS   0.006   0.001   HIS B  95 
 PHE   0.018   0.001   PHE B 237 
 TYR   0.019   0.001   TYR A 579 
 ARG   0.008   0.000   ARG B 246 

*********************** 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
  205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 173
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 ARG cc_start: 0.5886 (mpt180) cc_final: 0.4466 (ttp-170)
REVERT: A  362 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7927 (mm-30)
REVERT: A  498 ASP cc_start: 0.7414 (t0) cc_final: 0.7155 (t0)
REVERT: B  323 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7956 (pp30)
REVERT: B  348 ASN cc_start: 0.7445 (t0) cc_final: 0.6754 (t0)
REVERT: B  351 TYR cc_start: 0.7746 (t80) cc_final: 0.7386 (t80)
REVERT: B  399 GLN cc_start: 0.7564 (tm-30) cc_final: 0.7241 (tm-30)
REVERT: B  447 THR cc_start: 0.8944 (p) cc_final: 0.8687 (t)
REVERT: B  563 HIS cc_start: 0.7041 (OUTLIER) cc_final: 0.6218 (p90)
  outliers start: 32
  outliers final: 27
  residues processed: 198
  average time/residue: 0.2289
  time to fit residues: 60.7595
Evaluate side-chains
  195 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 167
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
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  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  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  142 VAL
Chi-restraints excluded: chain B residue  164 LEU
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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 101 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 35 optimal weight:    0.2980
   chunk 49 optimal weight:    5.9990
   chunk 41 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0170
   chunk 16 optimal weight:    0.9980
   chunk 100 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.4818

-------------------------------------------------------------------------------
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 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 = 0.4227 r_free = 0.4227 target = 0.174174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.138551 restraints weight = 11341.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.140768 restraints weight = 7017.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.142275 restraints weight = 4630.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7128
moved from start:          0.3677

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= 0.206
  Angle     :  0.781  16.576  12108  Z= 0.378
  Chirality :  0.045   0.297   1424
  Planarity :  0.005   0.049   1545
  Dihedral  :  5.434  32.825   1230
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 27.08 %
    Favored  : 69.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.26), residues: 1129
  helix:  0.69 (0.20), residues: 736
  sheet: -2.05 (0.63), residues: 64
  loop : -2.48 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 429 
 HIS   0.004   0.001   HIS B 248 
 PHE   0.024   0.001   PHE B 213 
 TYR   0.016   0.001   TYR A 579 
 ARG   0.013   0.001   ARG B 246 

********************** 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
  201 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 170
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 ARG cc_start: 0.5828 (mpt180) cc_final: 0.4470 (ttp-170)
REVERT: A  559 MET cc_start: 0.6650 (mmm) cc_final: 0.6287 (mmm)
REVERT: B  113 ARG cc_start: 0.7284 (mtt90) cc_final: 0.6859 (mtm-85)
REVERT: B  217 MET cc_start: 0.2604 (mtp) cc_final: 0.2041 (mtp)
REVERT: B  323 GLN cc_start: 0.8333 (tm-30) cc_final: 0.7978 (pp30)
REVERT: B  348 ASN cc_start: 0.7510 (t0) cc_final: 0.6794 (t0)
REVERT: B  351 TYR cc_start: 0.7773 (t80) cc_final: 0.7325 (t80)
REVERT: B  399 GLN cc_start: 0.7528 (tm-30) cc_final: 0.7238 (tm-30)
REVERT: B  563 HIS cc_start: 0.7038 (OUTLIER) cc_final: 0.6220 (p-80)
  outliers start: 31
  outliers final: 28
  residues processed: 195
  average time/residue: 0.2389
  time to fit residues: 62.1808
Evaluate side-chains
  194 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 165
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
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  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  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  142 VAL
Chi-restraints excluded: chain B residue  164 LEU
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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 106 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 86 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   overall best weight:    0.9380

-------------------------------------------------------------------------------
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 427 ASN ** 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 = 0.4200 r_free = 0.4200 target = 0.171497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.135465 restraints weight = 11375.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.137518 restraints weight = 7373.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.139712 restraints weight = 5115.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.3666

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= 0.258
  Angle     :  0.805  16.486  12108  Z= 0.389
  Chirality :  0.046   0.329   1424
  Planarity :  0.005   0.048   1545
  Dihedral  :  5.516  33.434   1230
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 26.64 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.25), residues: 1129
  helix:  0.56 (0.20), residues: 734
  sheet: -2.10 (0.63), residues: 64
  loop : -2.56 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 429 
 HIS   0.003   0.001   HIS A 578 
 PHE   0.017   0.002   PHE B 237 
 TYR   0.017   0.002   TYR B  92 
 ARG   0.008   0.001   ARG B 113 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2810.95 seconds
wall clock time: 51 minutes 2.93 seconds (3062.93 seconds total)