Starting phenix.real_space_refine
on Fri Jan 17 05:00:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yo5_39436/01_2025/8yo5_39436.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yo5_39436/01_2025/8yo5_39436.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yo5_39436/01_2025/8yo5_39436.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yo5_39436/01_2025/8yo5_39436.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yo5_39436/01_2025/8yo5_39436.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yo5_39436/01_2025/8yo5_39436.cif"
  }
  resolution = 3.93
  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=  -0.001 sd=   0.051
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      36      5.16       5
     C    6624      2.51       5
     N    1752      2.21       5
     O    1930      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 10342
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 442, 3563
          Classifications: {'peptide': 442}
          Link IDs: {'PTRANS': 13, 'TRANS': 428}
    Chain: "B"
      Number of atoms: 3563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 442, 3563
          Classifications: {'peptide': 442}
          Link IDs: {'PTRANS': 13, 'TRANS': 428}
    Chain: "C"
      Number of atoms: 1608
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1608
          Classifications: {'peptide': 200}
          Link IDs: {'PTRANS': 7, 'TRANS': 192}
    Chain: "D"
      Number of atoms: 1608
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1608
          Classifications: {'peptide': 200}
          Link IDs: {'PTRANS': 7, 'TRANS': 192}
  Time building chain proxies: 6.50, per 1000 atoms: 0.63
  Number of scatterers: 10342
  At special positions: 0
  Unit cell: (121.68, 100.88, 113.36, 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      36     16.00
     O    1930      8.00
     N    1752      7.00
     C    6624      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: 2.49
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2400

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 14 sheets defined
      45.0% alpha, 8.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 11
      No H-bonds generated for 'chain 'A' and resid 9 through 11'
    Processing helix  chain 'A' and resid 12 through 23
      removed outlier: 3.731A  pdb=" N   ALA A  16 " --> pdb=" O   ILE A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 52
      removed outlier: 3.687A  pdb=" N   PHE A  42 " --> pdb=" O   PRO A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 67
      removed outlier: 3.664A  pdb=" N   GLY A  67 " --> pdb=" O   SER A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 70
      No H-bonds generated for 'chain 'A' and resid 68 through 70'
    Processing helix  chain 'A' and resid 76 through 84
      removed outlier: 4.259A  pdb=" N   ALA A  80 " --> pdb=" O   GLY A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 128
      removed outlier: 3.987A  pdb=" N   TYR A 127 " --> pdb=" O   SER A 123 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ASN A 128 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 123 through 128'
    Processing helix  chain 'A' and resid 132 through 136
      removed outlier: 3.755A  pdb=" N   TYR A 135 " --> pdb=" O   ASP A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 190
      removed outlier: 3.911A  pdb=" N   GLN A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 254
      removed outlier: 5.035A  pdb=" N   ASP A 249 " --> pdb=" O   SER A 245 " (cutoff:3.500A)
      Proline residue:  A 250  - end of helix
    Processing helix  chain 'A' and resid 285 through 295
    Processing helix  chain 'A' and resid 319 through 366
      removed outlier: 3.927A  pdb=" N   LEU A 323 " --> pdb=" O   ASN A 319 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   THR A 333 " --> pdb=" O   GLU A 329 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ARG A 338 " --> pdb=" O   TYR A 334 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER A 348 " --> pdb=" O   LYS A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 375
      No H-bonds generated for 'chain 'A' and resid 373 through 375'
    Processing helix  chain 'A' and resid 376 through 383
      removed outlier: 4.490A  pdb=" N   GLU A 380 " --> pdb=" O   LYS A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 390
      removed outlier: 3.764A  pdb=" N   SER A 390 " --> pdb=" O   MET A 387 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 387 through 390'
    Processing helix  chain 'A' and resid 391 through 396
    Processing helix  chain 'A' and resid 399 through 403
    Processing helix  chain 'A' and resid 404 through 428
      removed outlier: 3.881A  pdb=" N   LYS A 410 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LEU A 411 " --> pdb=" O   GLU A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 441
      removed outlier: 3.578A  pdb=" N   ILE A 441 " --> pdb=" O   ASP A 437 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 11
    Processing helix  chain 'B' and resid 12 through 23
      removed outlier: 3.704A  pdb=" N   ALA B  16 " --> pdb=" O   ILE B  12 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 52
      removed outlier: 3.730A  pdb=" N   PHE B  42 " --> pdb=" O   PRO B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 67
      removed outlier: 3.788A  pdb=" N   GLY B  67 " --> pdb=" O   SER B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 84
      removed outlier: 4.249A  pdb=" N   ALA B  80 " --> pdb=" O   GLY B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 128
      removed outlier: 3.985A  pdb=" N   TYR B 127 " --> pdb=" O   SER B 123 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ASN B 128 " --> pdb=" O   LYS B 124 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 123 through 128'
    Processing helix  chain 'B' and resid 132 through 136
      removed outlier: 3.754A  pdb=" N   TYR B 135 " --> pdb=" O   ASP B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 190
      removed outlier: 3.906A  pdb=" N   GLN B 190 " --> pdb=" O   LEU B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 247
    Processing helix  chain 'B' and resid 247 through 254
    Processing helix  chain 'B' and resid 285 through 295
      removed outlier: 3.837A  pdb=" N   PHE B 295 " --> pdb=" O   ILE B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 366
      removed outlier: 3.918A  pdb=" N   LEU B 323 " --> pdb=" O   ASN B 319 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   THR B 333 " --> pdb=" O   GLU B 329 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ARG B 338 " --> pdb=" O   TYR B 334 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   SER B 348 " --> pdb=" O   LYS B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 383
      removed outlier: 3.978A  pdb=" N   GLU B 380 " --> pdb=" O   LYS B 376 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 390
      removed outlier: 3.760A  pdb=" N   SER B 390 " --> pdb=" O   MET B 387 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 387 through 390'
    Processing helix  chain 'B' and resid 391 through 397
    Processing helix  chain 'B' and resid 399 through 404
      removed outlier: 3.884A  pdb=" N   THR B 404 " --> pdb=" O   PHE B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 428
      removed outlier: 3.813A  pdb=" N   LYS B 410 " --> pdb=" O   ASP B 406 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   LEU B 411 " --> pdb=" O   GLU B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 441
      removed outlier: 3.576A  pdb=" N   ILE B 441 " --> pdb=" O   ASP B 437 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 427
    Processing helix  chain 'C' and resid 448 through 455
      removed outlier: 4.073A  pdb=" N   ASN C 455 " --> pdb=" O   ASP C 451 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 455 through 466
    Processing helix  chain 'C' and resid 494 through 504
      removed outlier: 4.054A  pdb=" N   SER C 498 " --> pdb=" O   SER C 494 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 506 through 513
      removed outlier: 3.687A  pdb=" N   PHE C 510 " --> pdb=" O   TRP C 506 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 536 through 544
    Processing helix  chain 'C' and resid 557 through 561
    Processing helix  chain 'C' and resid 562 through 572
    Processing helix  chain 'C' and resid 585 through 590
    Processing helix  chain 'D' and resid 416 through 427
    Processing helix  chain 'D' and resid 448 through 455
      removed outlier: 3.783A  pdb=" N   ASN D 455 " --> pdb=" O   ASP D 451 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 455 through 466
    Processing helix  chain 'D' and resid 494 through 504
      removed outlier: 3.918A  pdb=" N   SER D 498 " --> pdb=" O   SER D 494 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 506 through 513
    Processing helix  chain 'D' and resid 536 through 544
    Processing helix  chain 'D' and resid 562 through 572
    Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 60
    Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 165
    Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 210
    Processing sheet with id=AA4, first strand: chain 'A' and resid 220 through 225
      removed outlier: 6.408A  pdb=" N   THR A 220 " --> pdb=" O   THR A 232 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LYS A 222 " --> pdb=" O   HIS A 230 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   GLN A 228 " --> pdb=" O   THR A 224 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LYS A 271 " --> pdb=" O   ASP A 260 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 308
    Processing sheet with id=AA6, first strand: chain 'B' and resid 59 through 60
    Processing sheet with id=AA7, first strand: chain 'B' and resid 162 through 165
    Processing sheet with id=AA8, first strand: chain 'B' and resid 207 through 209
    Processing sheet with id=AA9, first strand: chain 'B' and resid 223 through 225
      removed outlier: 5.790A  pdb=" N   PHE B 223 " --> pdb=" O   HIS B 230 " (cutoff:3.500A)
      removed outlier: 5.854A  pdb=" N   HIS B 230 " --> pdb=" O   PHE B 223 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLN B 228 " --> pdb=" O   SER B 225 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LYS B 271 " --> pdb=" O   ASP B 260 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 306 through 308
    Processing sheet with id=AB2, first strand: chain 'C' and resid 410 through 414
      removed outlier: 5.918A  pdb=" N   LEU C 411 " --> pdb=" O   ALA C 482 " (cutoff:3.500A)
      removed outlier: 7.176A  pdb=" N   MET C 484 " --> pdb=" O   LEU C 411 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   LEU C 413 " --> pdb=" O   MET C 484 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ILE C 481 " --> pdb=" O   ARG C 516 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 523 through 526
      removed outlier: 4.149A  pdb=" N   SER C 551 " --> pdb=" O   HIS C 526 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 435 through 437
      removed outlier: 7.349A  pdb=" N   TYR D 435 " --> pdb=" O   THR D 410 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   PHE D 412 " --> pdb=" O   TYR D 435 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   LEU D 437 " --> pdb=" O   PHE D 412 " (cutoff:3.500A)
      removed outlier: 7.539A  pdb=" N   THR D 414 " --> pdb=" O   LEU D 437 " (cutoff:3.500A)
      removed outlier: 5.653A  pdb=" N   LEU D 411 " --> pdb=" O   ALA D 482 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   ILE D 481 " --> pdb=" O   ARG D 516 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   VAL D 518 " --> pdb=" O   ILE D 481 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   ILE D 483 " --> pdb=" O   VAL D 518 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 530 through 532
      removed outlier: 3.538A  pdb=" N   SER D 551 " --> pdb=" O   HIS D 526 " (cutoff:3.500A)

    396 hydrogen bonds defined for protein.
    1122 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: 3.27

  Time building geometry restraints manager: 2.90 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3346
        1.34 -     1.46: 2363
        1.46 -     1.58: 4789
        1.58 -     1.70: 0
        1.70 -     1.82: 66
  Bond restraints: 10564
  Sorted by residual:
  bond pdb=" CB  LYS A 142 "
       pdb=" CG  LYS A 142 "
    ideal  model  delta    sigma   weight residual
    1.520  1.557 -0.037 3.00e-02 1.11e+03 1.53e+00
  bond pdb=" CB  MET C 590 "
       pdb=" CG  MET C 590 "
    ideal  model  delta    sigma   weight residual
    1.520  1.557 -0.037 3.00e-02 1.11e+03 1.49e+00
  bond pdb=" CB  PRO D 581 "
       pdb=" CG  PRO D 581 "
    ideal  model  delta    sigma   weight residual
    1.492  1.549 -0.057 5.00e-02 4.00e+02 1.29e+00
  bond pdb=" CA  LEU B   3 "
       pdb=" CB  LEU B   3 "
    ideal  model  delta    sigma   weight residual
    1.525  1.540 -0.015 1.29e-02 6.01e+03 1.28e+00
  bond pdb=" CB  PRO D 436 "
       pdb=" CG  PRO D 436 "
    ideal  model  delta    sigma   weight residual
    1.492  1.548 -0.056 5.00e-02 4.00e+02 1.25e+00
  ... (remaining 10559 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.98: 14147
        2.98 -     5.96: 81
        5.96 -     8.94: 10
        8.94 -    11.93: 1
       11.93 -    14.91: 1
  Bond angle restraints: 14240
  Sorted by residual:
  angle pdb=" CA  LEU B   3 "
        pdb=" CB  LEU B   3 "
        pdb=" CG  LEU B   3 "
      ideal   model   delta    sigma   weight residual
     116.30  131.21  -14.91 3.50e+00 8.16e-02 1.81e+01
  angle pdb=" CA  MET C 452 "
        pdb=" CB  MET C 452 "
        pdb=" CG  MET C 452 "
      ideal   model   delta    sigma   weight residual
     114.10  121.07   -6.97 2.00e+00 2.50e-01 1.21e+01
  angle pdb=" CA  LYS A 142 "
        pdb=" CB  LYS A 142 "
        pdb=" CG  LYS A 142 "
      ideal   model   delta    sigma   weight residual
     114.10  120.45   -6.35 2.00e+00 2.50e-01 1.01e+01
  angle pdb=" CB  LYS A 142 "
        pdb=" CG  LYS A 142 "
        pdb=" CD  LYS A 142 "
      ideal   model   delta    sigma   weight residual
     111.30  118.31   -7.01 2.30e+00 1.89e-01 9.29e+00
  angle pdb=" CA  MET C 590 "
        pdb=" CB  MET C 590 "
        pdb=" CG  MET C 590 "
      ideal   model   delta    sigma   weight residual
     114.10  119.88   -5.78 2.00e+00 2.50e-01 8.37e+00
  ... (remaining 14235 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.16: 5193
       17.16 -    34.32: 866
       34.32 -    51.48: 222
       51.48 -    68.64: 61
       68.64 -    85.80: 20
  Dihedral angle restraints: 6362
    sinusoidal: 2618
      harmonic: 3744
  Sorted by residual:
  dihedral pdb=" CA  ASP C 451 "
           pdb=" C   ASP C 451 "
           pdb=" N   MET C 452 "
           pdb=" CA  MET C 452 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.19   23.81     0      5.00e+00 4.00e-02 2.27e+01
  dihedral pdb=" CA  ALA C 487 "
           pdb=" C   ALA C 487 "
           pdb=" N   ASP C 488 "
           pdb=" CA  ASP C 488 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.62   21.38     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  ALA D 487 "
           pdb=" C   ALA D 487 "
           pdb=" N   ASP D 488 "
           pdb=" CA  ASP D 488 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.36   20.64     0      5.00e+00 4.00e-02 1.70e+01
  ... (remaining 6359 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1217
       0.048 -    0.095: 257
       0.095 -    0.143: 63
       0.143 -    0.191: 2
       0.191 -    0.238: 1
  Chirality restraints: 1540
  Sorted by residual:
  chirality pdb=" CB  VAL C 577 "
            pdb=" CA  VAL C 577 "
            pdb=" CG1 VAL C 577 "
            pdb=" CG2 VAL C 577 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CA  ASP B  34 "
            pdb=" N   ASP B  34 "
            pdb=" C   ASP B  34 "
            pdb=" CB  ASP B  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.23e-01
  chirality pdb=" CG  LEU B   3 "
            pdb=" CB  LEU B   3 "
            pdb=" CD1 LEU B   3 "
            pdb=" CD2 LEU B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 5.23e-01
  ... (remaining 1537 not shown)

  Planarity restraints: 1822
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP C 506 "   -0.037 5.00e-02 4.00e+02   5.70e-02 5.19e+00
        pdb=" N   PRO C 507 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO C 507 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO C 507 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP D 506 "    0.035 5.00e-02 4.00e+02   5.36e-02 4.59e+00
        pdb=" N   PRO D 507 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO D 507 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO D 507 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 244 "   -0.010 2.00e-02 2.50e+03   1.99e-02 3.95e+00
        pdb=" C   VAL B 244 "    0.034 2.00e-02 2.50e+03
        pdb=" O   VAL B 244 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   SER B 245 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1819 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 246
        2.68 -     3.24: 10593
        3.24 -     3.79: 16299
        3.79 -     4.35: 20827
        4.35 -     4.90: 33560
  Nonbonded interactions: 81525
  Sorted by model distance:
  nonbonded pdb=" O   ASP B  34 "
            pdb=" OH  TYR B 130 "
     model   vdw
     2.130 3.040
  nonbonded pdb=" O   ASP A  34 "
            pdb=" OH  TYR A 130 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" O   PHE C 502 "
            pdb=" ND2 ASN C 505 "
     model   vdw
     2.159 3.120
  nonbonded pdb=" O   HIS C 526 "
            pdb=" OG  SER C 551 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" OD1 ASP A 239 "
            pdb=" OG1 THR A 242 "
     model   vdw
     2.195 3.040
  ... (remaining 81520 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.430
  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:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.900
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10564  Z= 0.189
  Angle     :  0.634  14.908  14240  Z= 0.334
  Chirality :  0.042   0.238   1540
  Planarity :  0.004   0.057   1822
  Dihedral  : 18.803  85.805   3962
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 38.54 %
    Favored  : 60.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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 (0.24), residues: 1276
  helix:  0.15 (0.24), residues: 504
  sheet: -1.61 (0.48), residues: 136
  loop : -1.68 (0.25), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP D 584 
 HIS   0.009   0.001   HIS B 288 
 PHE   0.027   0.002   PHE A 274 
 TYR   0.017   0.001   TYR B 388 
 ARG   0.007   0.001   ARG D 438 

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 178
  time to evaluate  : 1.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 TYR cc_start: 0.8083 (m-10) cc_final: 0.7733 (m-10)
REVERT: B  398 MET cc_start: 0.7377 (mmp) cc_final: 0.7060 (mmm)
REVERT: C  590 MET cc_start: 0.8197 (tmm) cc_final: 0.7938 (mmm)
  outliers start: 6
  outliers final: 3
  residues processed: 178
  average time/residue: 0.2187
  time to fit residues: 55.6907
Evaluate side-chains
  166 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 163
  time to evaluate  : 1.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 TRP
Chi-restraints excluded: chain B residue   19 TYR
Chi-restraints excluded: chain D residue  537 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.2980
   chunk 51 optimal weight:    0.3980
   chunk 100 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 116 optimal weight:    5.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
** B   5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 480 ASN
D 432 HIS
D 480 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.127386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.094032 restraints weight = 22247.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.096659 restraints weight = 14344.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.098394 restraints weight = 10844.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.0829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10564  Z= 0.190
  Angle     :  0.573  10.693  14240  Z= 0.297
  Chirality :  0.042   0.165   1540
  Planarity :  0.004   0.045   1822
  Dihedral  :  4.812  46.534   1401
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 33.21 %
    Favored  : 61.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.10 (0.24), residues: 1276
  helix:  0.67 (0.24), residues: 504
  sheet: -1.73 (0.50), residues: 128
  loop : -1.68 (0.25), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP C 445 
 HIS   0.009   0.001   HIS B 288 
 PHE   0.020   0.001   PHE B 274 
 TYR   0.011   0.001   TYR C 496 
 ARG   0.005   0.001   ARG D 438 

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 171
  time to evaluate  : 1.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LYS cc_start: 0.9151 (mtpp) cc_final: 0.8842 (mtpp)
REVERT: A  388 TYR cc_start: 0.8177 (m-10) cc_final: 0.7793 (m-10)
REVERT: B  387 MET cc_start: 0.8641 (pmm) cc_final: 0.7957 (pmm)
REVERT: B  398 MET cc_start: 0.7580 (mmp) cc_final: 0.7298 (mmm)
REVERT: C  422 TYR cc_start: 0.8253 (m-80) cc_final: 0.7362 (t80)
REVERT: C  431 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8450 (mp)
REVERT: C  531 GLN cc_start: 0.7134 (pm20) cc_final: 0.6867 (pm20)
REVERT: D  496 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7901 (m-80)
  outliers start: 54
  outliers final: 27
  residues processed: 205
  average time/residue: 0.2110
  time to fit residues: 62.5064
Evaluate side-chains
  184 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 155
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue  205 ARG
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  254 LYS
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  381 GLU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain B residue   32 MET
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain C residue  420 ILE
Chi-restraints excluded: chain C residue  426 VAL
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  518 VAL
Chi-restraints excluded: chain D residue  422 TYR
Chi-restraints excluded: chain D residue  441 VAL
Chi-restraints excluded: chain D residue  445 TRP
Chi-restraints excluded: chain D residue  447 MET
Chi-restraints excluded: chain D residue  468 VAL
Chi-restraints excluded: chain D residue  496 TYR
Chi-restraints excluded: chain D residue  518 VAL
Chi-restraints excluded: chain D residue  527 VAL
Chi-restraints excluded: chain D residue  558 LEU
Chi-restraints excluded: chain D residue  560 SER
Chi-restraints excluded: chain D residue  578 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 113 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 63 optimal weight:    0.1980
   chunk 110 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   chunk 98 optimal weight:    0.0170
   chunk 35 optimal weight:    0.8980
   chunk 114 optimal weight:    0.9990
   chunk 125 optimal weight:    0.8980
   chunk 116 optimal weight:    5.9990
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
** B   5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.128034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.094900 restraints weight = 22238.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.097542 restraints weight = 14173.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.099207 restraints weight = 10647.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.1130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10564  Z= 0.171
  Angle     :  0.547   9.571  14240  Z= 0.280
  Chirality :  0.041   0.138   1540
  Planarity :  0.003   0.041   1822
  Dihedral  :  4.442  20.838   1396
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 32.49 %
    Favored  : 62.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -1.07 (0.24), residues: 1276
  helix:  0.65 (0.24), residues: 514
  sheet: -1.65 (0.50), residues: 124
  loop : -1.69 (0.25), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 445 
 HIS   0.009   0.001   HIS B 288 
 PHE   0.018   0.001   PHE C 588 
 TYR   0.011   0.001   TYR B 278 
 ARG   0.003   0.000   ARG A 226 

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 174
  time to evaluate  : 1.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.8158 (t80)
REVERT: A  254 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8516 (mmtm)
REVERT: A  292 MET cc_start: 0.8425 (mmm) cc_final: 0.8209 (mmm)
REVERT: A  388 TYR cc_start: 0.8308 (m-10) cc_final: 0.7853 (m-10)
REVERT: B   21 MET cc_start: 0.8379 (mmp) cc_final: 0.8092 (mmp)
REVERT: B   95 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.8080 (t80)
REVERT: B  142 LYS cc_start: 0.8537 (tppt) cc_final: 0.8323 (tppt)
REVERT: B  229 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8425 (pmm)
REVERT: B  387 MET cc_start: 0.8637 (pmm) cc_final: 0.7987 (pmm)
REVERT: B  388 TYR cc_start: 0.7927 (m-10) cc_final: 0.7540 (m-10)
REVERT: B  402 HIS cc_start: 0.8425 (OUTLIER) cc_final: 0.7986 (t-90)
REVERT: C  422 TYR cc_start: 0.8178 (m-80) cc_final: 0.7363 (t80)
REVERT: C  590 MET cc_start: 0.8054 (tmm) cc_final: 0.7663 (mmm)
REVERT: D  438 ARG cc_start: 0.8498 (tmm160) cc_final: 0.8284 (ttp80)
REVERT: D  496 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.7921 (m-80)
  outliers start: 58
  outliers final: 34
  residues processed: 210
  average time/residue: 0.2327
  time to fit residues: 69.0569
Evaluate side-chains
  195 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 155
  time to evaluate  : 1.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 TYR
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  254 LYS
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   32 MET
Chi-restraints excluded: chain B residue   60 LYS
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  247 ILE
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  402 HIS
Chi-restraints excluded: chain C residue  420 ILE
Chi-restraints excluded: chain C residue  426 VAL
Chi-restraints excluded: chain C residue  518 VAL
Chi-restraints excluded: chain D residue  422 TYR
Chi-restraints excluded: chain D residue  445 TRP
Chi-restraints excluded: chain D residue  447 MET
Chi-restraints excluded: chain D residue  468 VAL
Chi-restraints excluded: chain D residue  496 TYR
Chi-restraints excluded: chain D residue  518 VAL
Chi-restraints excluded: chain D residue  527 VAL
Chi-restraints excluded: chain D residue  537 VAL
Chi-restraints excluded: chain D residue  558 LEU
Chi-restraints excluded: chain D residue  560 SER
Chi-restraints excluded: chain D residue  578 VAL
Chi-restraints excluded: chain D residue  583 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 107 optimal weight:    0.0970
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 63 optimal weight:    0.6980
   chunk 81 optimal weight:    2.9990
   chunk 116 optimal weight:    1.9990
   chunk 96 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   chunk 120 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 402 HIS
** B   5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.125320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.095904 restraints weight = 22367.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.096133 restraints weight = 16919.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.096757 restraints weight = 17340.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.1436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10564  Z= 0.250
  Angle     :  0.570   9.878  14240  Z= 0.294
  Chirality :  0.042   0.183   1540
  Planarity :  0.004   0.038   1822
  Dihedral  :  4.500  21.301   1396
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  6.86 %
    Allowed  : 31.23 %
    Favored  : 61.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.16 (0.24), residues: 1276
  helix:  0.61 (0.23), residues: 520
  sheet: -1.98 (0.48), residues: 128
  loop : -1.72 (0.25), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 445 
 HIS   0.009   0.001   HIS B 288 
 PHE   0.015   0.002   PHE D 502 
 TYR   0.012   0.001   TYR A 278 
 ARG   0.006   0.000   ARG B 240 

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 158
  time to evaluate  : 1.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8328 (t80)
REVERT: A  292 MET cc_start: 0.8685 (mmm) cc_final: 0.8459 (mmm)
REVERT: A  327 PHE cc_start: 0.8823 (t80) cc_final: 0.8423 (t80)
REVERT: B   21 MET cc_start: 0.8349 (mmp) cc_final: 0.8116 (mmp)
REVERT: B   95 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8252 (t80)
REVERT: B  229 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8416 (pmm)
REVERT: B  292 MET cc_start: 0.7464 (mtm) cc_final: 0.7247 (mtm)
REVERT: B  327 PHE cc_start: 0.8721 (t80) cc_final: 0.8369 (t80)
REVERT: B  388 TYR cc_start: 0.8166 (m-10) cc_final: 0.7792 (m-10)
REVERT: B  402 HIS cc_start: 0.8461 (OUTLIER) cc_final: 0.8040 (t-90)
REVERT: C  422 TYR cc_start: 0.8217 (m-80) cc_final: 0.7450 (t80)
REVERT: D  438 ARG cc_start: 0.8550 (tmm160) cc_final: 0.8286 (ttp80)
REVERT: D  496 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7921 (m-80)
  outliers start: 76
  outliers final: 49
  residues processed: 210
  average time/residue: 0.2038
  time to fit residues: 61.7766
Evaluate side-chains
  204 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 150
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 TYR
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  205 ARG
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  254 LYS
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  350 PHE
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   32 MET
Chi-restraints excluded: chain B residue   60 LYS
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  247 ILE
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  402 HIS
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain C residue  420 ILE
Chi-restraints excluded: chain C residue  426 VAL
Chi-restraints excluded: chain C residue  518 VAL
Chi-restraints excluded: chain C residue  520 THR
Chi-restraints excluded: chain D residue  395 HIS
Chi-restraints excluded: chain D residue  403 CYS
Chi-restraints excluded: chain D residue  422 TYR
Chi-restraints excluded: chain D residue  441 VAL
Chi-restraints excluded: chain D residue  445 TRP
Chi-restraints excluded: chain D residue  447 MET
Chi-restraints excluded: chain D residue  468 VAL
Chi-restraints excluded: chain D residue  483 ILE
Chi-restraints excluded: chain D residue  496 TYR
Chi-restraints excluded: chain D residue  518 VAL
Chi-restraints excluded: chain D residue  527 VAL
Chi-restraints excluded: chain D residue  537 VAL
Chi-restraints excluded: chain D residue  558 LEU
Chi-restraints excluded: chain D residue  560 SER
Chi-restraints excluded: chain D residue  578 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 126 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 113 optimal weight:    0.0060
   chunk 84 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   chunk 55 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0010
   chunk 115 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.4602

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

Flipped N/Q/H residues before XYZ refinement:
** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.127008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.098212 restraints weight = 22571.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.098809 restraints weight = 17019.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.099283 restraints weight = 16921.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10564  Z= 0.165
  Angle     :  0.556  11.234  14240  Z= 0.280
  Chirality :  0.041   0.160   1540
  Planarity :  0.003   0.037   1822
  Dihedral  :  4.442  23.073   1396
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 32.13 %
    Favored  : 62.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.02 (0.24), residues: 1276
  helix:  0.80 (0.24), residues: 504
  sheet: -1.90 (0.49), residues: 128
  loop : -1.66 (0.25), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 584 
 HIS   0.008   0.001   HIS B 288 
 PHE   0.021   0.001   PHE C 588 
 TYR   0.011   0.001   TYR B 388 
 ARG   0.004   0.000   ARG B 240 

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 165
  time to evaluate  : 1.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LYS cc_start: 0.9144 (mtpp) cc_final: 0.8924 (mtpp)
REVERT: A   95 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.8250 (t80)
REVERT: A  292 MET cc_start: 0.8708 (mmm) cc_final: 0.8497 (mmm)
REVERT: A  387 MET cc_start: 0.8797 (pmm) cc_final: 0.8238 (pmm)
REVERT: B   37 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8628 (mtmm)
REVERT: B   60 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8861 (mtpp)
REVERT: B   95 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.8147 (t80)
REVERT: B  229 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8430 (pmm)
REVERT: B  387 MET cc_start: 0.8743 (pmm) cc_final: 0.8268 (pmm)
REVERT: B  402 HIS cc_start: 0.8475 (OUTLIER) cc_final: 0.8021 (t-90)
REVERT: C  422 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7432 (t80)
REVERT: C  590 MET cc_start: 0.8000 (tmm) cc_final: 0.7696 (mmm)
REVERT: D  438 ARG cc_start: 0.8536 (tmm160) cc_final: 0.8275 (ttp80)
REVERT: D  496 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.7901 (m-80)
REVERT: D  510 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7419 (t80)
  outliers start: 56
  outliers final: 33
  residues processed: 196
  average time/residue: 0.2023
  time to fit residues: 57.7808
Evaluate side-chains
  190 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 148
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 TYR
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   19 TYR
Chi-restraints excluded: chain B residue   32 MET
Chi-restraints excluded: chain B residue   37 LYS
Chi-restraints excluded: chain B residue   60 LYS
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  402 HIS
Chi-restraints excluded: chain C residue  420 ILE
Chi-restraints excluded: chain C residue  422 TYR
Chi-restraints excluded: chain C residue  426 VAL
Chi-restraints excluded: chain C residue  517 PHE
Chi-restraints excluded: chain C residue  518 VAL
Chi-restraints excluded: chain D residue  422 TYR
Chi-restraints excluded: chain D residue  445 TRP
Chi-restraints excluded: chain D residue  447 MET
Chi-restraints excluded: chain D residue  468 VAL
Chi-restraints excluded: chain D residue  483 ILE
Chi-restraints excluded: chain D residue  496 TYR
Chi-restraints excluded: chain D residue  510 PHE
Chi-restraints excluded: chain D residue  518 VAL
Chi-restraints excluded: chain D residue  527 VAL
Chi-restraints excluded: chain D residue  558 LEU
Chi-restraints excluded: chain D residue  560 SER
Chi-restraints excluded: chain D residue  583 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0570
   chunk 46 optimal weight:    7.9990
   chunk 104 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 67 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    1.1502

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

Flipped N/Q/H residues before XYZ refinement:
** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.124008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.095019 restraints weight = 22564.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.095854 restraints weight = 17124.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.096097 restraints weight = 18412.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10564  Z= 0.248
  Angle     :  0.582  10.105  14240  Z= 0.297
  Chirality :  0.042   0.139   1540
  Planarity :  0.003   0.039   1822
  Dihedral  :  4.575  34.282   1396
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 32.67 %
    Favored  : 61.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.11 (0.24), residues: 1276
  helix:  0.76 (0.23), residues: 506
  sheet: -1.94 (0.49), residues: 128
  loop : -1.75 (0.24), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 584 
 HIS   0.008   0.001   HIS B 288 
 PHE   0.017   0.002   PHE C 502 
 TYR   0.012   0.001   TYR B 388 
 ARG   0.003   0.000   ARG A 226 

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 150
  time to evaluate  : 1.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6920 (pmm)
REVERT: A   95 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8344 (t80)
REVERT: A  229 MET cc_start: 0.9230 (pmm) cc_final: 0.8675 (pmm)
REVERT: A  292 MET cc_start: 0.8777 (mmm) cc_final: 0.8542 (mmm)
REVERT: A  327 PHE cc_start: 0.8886 (t80) cc_final: 0.8529 (t80)
REVERT: A  387 MET cc_start: 0.8848 (pmm) cc_final: 0.8300 (pmm)
REVERT: A  404 THR cc_start: 0.7870 (m) cc_final: 0.7252 (p)
REVERT: B   95 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8310 (t80)
REVERT: B  229 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8314 (pmm)
REVERT: B  231 ILE cc_start: 0.8887 (mm) cc_final: 0.8569 (mt)
REVERT: B  292 MET cc_start: 0.7689 (mtm) cc_final: 0.7306 (mtm)
REVERT: B  327 PHE cc_start: 0.8827 (t80) cc_final: 0.8492 (t80)
REVERT: B  387 MET cc_start: 0.8819 (pmm) cc_final: 0.8352 (pmm)
REVERT: B  402 HIS cc_start: 0.8422 (OUTLIER) cc_final: 0.8007 (t-90)
REVERT: C  422 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7497 (t80)
REVERT: D  438 ARG cc_start: 0.8545 (tmm160) cc_final: 0.8259 (ttp80)
REVERT: D  496 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.8038 (m-80)
  outliers start: 66
  outliers final: 46
  residues processed: 195
  average time/residue: 0.2097
  time to fit residues: 58.8448
Evaluate side-chains
  196 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 143
  time to evaluate  : 1.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  205 ARG
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  254 LYS
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain B residue    6 ARG
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   32 MET
Chi-restraints excluded: chain B residue   60 LYS
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  247 ILE
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  402 HIS
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain C residue  420 ILE
Chi-restraints excluded: chain C residue  422 TYR
Chi-restraints excluded: chain C residue  426 VAL
Chi-restraints excluded: chain C residue  441 VAL
Chi-restraints excluded: chain C residue  517 PHE
Chi-restraints excluded: chain C residue  518 VAL
Chi-restraints excluded: chain C residue  520 THR
Chi-restraints excluded: chain C residue  552 ILE
Chi-restraints excluded: chain C residue  564 SER
Chi-restraints excluded: chain D residue  403 CYS
Chi-restraints excluded: chain D residue  422 TYR
Chi-restraints excluded: chain D residue  445 TRP
Chi-restraints excluded: chain D residue  447 MET
Chi-restraints excluded: chain D residue  468 VAL
Chi-restraints excluded: chain D residue  483 ILE
Chi-restraints excluded: chain D residue  496 TYR
Chi-restraints excluded: chain D residue  499 LEU
Chi-restraints excluded: chain D residue  518 VAL
Chi-restraints excluded: chain D residue  520 THR
Chi-restraints excluded: chain D residue  558 LEU
Chi-restraints excluded: chain D residue  560 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 64 optimal weight:    0.0170
   chunk 78 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   chunk 118 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 125 optimal weight:    0.8980
   chunk 82 optimal weight:    0.7980
   chunk 93 optimal weight:    0.0060
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.5234

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

Flipped N/Q/H residues before XYZ refinement:
** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.125895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.097051 restraints weight = 22580.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.098201 restraints weight = 16469.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.098668 restraints weight = 15182.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10564  Z= 0.174
  Angle     :  0.571   9.976  14240  Z= 0.288
  Chirality :  0.041   0.138   1540
  Planarity :  0.003   0.038   1822
  Dihedral  :  4.511  32.892   1396
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 33.94 %
    Favored  : 61.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.03 (0.24), residues: 1276
  helix:  0.79 (0.24), residues: 506
  sheet: -1.88 (0.49), residues: 128
  loop : -1.68 (0.25), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D 584 
 HIS   0.007   0.001   HIS B 288 
 PHE   0.017   0.001   PHE D 517 
 TYR   0.010   0.001   TYR B 388 
 ARG   0.003   0.000   ARG B 226 

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 158
  time to evaluate  : 1.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8162 (t80)
REVERT: A  229 MET cc_start: 0.9152 (pmm) cc_final: 0.8613 (pmm)
REVERT: A  292 MET cc_start: 0.8762 (mmm) cc_final: 0.8535 (mmm)
REVERT: A  387 MET cc_start: 0.8836 (pmm) cc_final: 0.8362 (pmm)
REVERT: A  404 THR cc_start: 0.7772 (m) cc_final: 0.7163 (p)
REVERT: B   37 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8639 (mtmm)
REVERT: B   95 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8191 (t80)
REVERT: B  142 LYS cc_start: 0.8627 (tppt) cc_final: 0.8414 (tppt)
REVERT: B  226 ARG cc_start: 0.8343 (mmp80) cc_final: 0.8128 (mmp80)
REVERT: B  229 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8398 (pmm)
REVERT: B  292 MET cc_start: 0.7484 (mtm) cc_final: 0.7055 (mtm)
REVERT: B  387 MET cc_start: 0.8768 (pmm) cc_final: 0.8428 (pmm)
REVERT: B  402 HIS cc_start: 0.8455 (OUTLIER) cc_final: 0.8009 (t-90)
REVERT: C  422 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7456 (t80)
REVERT: C  590 MET cc_start: 0.7956 (tmm) cc_final: 0.7600 (mmm)
REVERT: D  438 ARG cc_start: 0.8564 (tmm160) cc_final: 0.8279 (ttp80)
REVERT: D  496 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.8072 (m-80)
REVERT: D  534 PHE cc_start: 0.7539 (m-10) cc_final: 0.7058 (m-10)
  outliers start: 50
  outliers final: 33
  residues processed: 189
  average time/residue: 0.2246
  time to fit residues: 60.6520
Evaluate side-chains
  188 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 148
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 TYR
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  205 ARG
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain B residue    6 ARG
Chi-restraints excluded: chain B residue   32 MET
Chi-restraints excluded: chain B residue   37 LYS
Chi-restraints excluded: chain B residue   60 LYS
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  232 THR
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  402 HIS
Chi-restraints excluded: chain C residue  420 ILE
Chi-restraints excluded: chain C residue  422 TYR
Chi-restraints excluded: chain C residue  426 VAL
Chi-restraints excluded: chain C residue  517 PHE
Chi-restraints excluded: chain C residue  518 VAL
Chi-restraints excluded: chain D residue  445 TRP
Chi-restraints excluded: chain D residue  447 MET
Chi-restraints excluded: chain D residue  468 VAL
Chi-restraints excluded: chain D residue  496 TYR
Chi-restraints excluded: chain D residue  499 LEU
Chi-restraints excluded: chain D residue  518 VAL
Chi-restraints excluded: chain D residue  520 THR
Chi-restraints excluded: chain D residue  558 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 116 optimal weight:    4.9990
   chunk 20 optimal weight:    0.3980
   chunk 42 optimal weight:    0.9980
   chunk 105 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 68 optimal weight:    0.0370
   chunk 124 optimal weight:    0.9980
   chunk 96 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
** B   5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 480 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.125746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.096909 restraints weight = 22162.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.097461 restraints weight = 16049.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.097995 restraints weight = 15873.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10564  Z= 0.187
  Angle     :  0.572  10.088  14240  Z= 0.288
  Chirality :  0.041   0.145   1540
  Planarity :  0.003   0.037   1822
  Dihedral  :  4.484  33.376   1396
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 33.94 %
    Favored  : 61.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.06 (0.24), residues: 1276
  helix:  0.78 (0.24), residues: 506
  sheet: -2.07 (0.45), residues: 148
  loop : -1.62 (0.25), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP D 584 
 HIS   0.007   0.001   HIS B 288 
 PHE   0.020   0.001   PHE C 502 
 TYR   0.013   0.001   TYR A 334 
 ARG   0.002   0.000   ARG B 240 

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 151
  time to evaluate  : 1.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.8154 (t80)
REVERT: A  229 MET cc_start: 0.9124 (pmm) cc_final: 0.8545 (pmm)
REVERT: A  292 MET cc_start: 0.8775 (mmm) cc_final: 0.8561 (mmm)
REVERT: A  387 MET cc_start: 0.8861 (pmm) cc_final: 0.8423 (pmm)
REVERT: A  404 THR cc_start: 0.7791 (m) cc_final: 0.7141 (p)
REVERT: B   37 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8701 (mtmm)
REVERT: B   95 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.8114 (t80)
REVERT: B  229 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8408 (pmm)
REVERT: B  231 ILE cc_start: 0.8837 (mm) cc_final: 0.8510 (mm)
REVERT: B  387 MET cc_start: 0.8791 (pmm) cc_final: 0.8503 (pmm)
REVERT: B  402 HIS cc_start: 0.8455 (OUTLIER) cc_final: 0.7993 (t-90)
REVERT: C  422 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7424 (t80)
REVERT: C  590 MET cc_start: 0.7999 (tmm) cc_final: 0.7672 (mmm)
REVERT: D  438 ARG cc_start: 0.8565 (tmm160) cc_final: 0.8283 (ttp80)
REVERT: D  496 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.8029 (m-80)
  outliers start: 53
  outliers final: 37
  residues processed: 188
  average time/residue: 0.2153
  time to fit residues: 58.3639
Evaluate side-chains
  193 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 149
  time to evaluate  : 1.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 TYR
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  205 ARG
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain B residue    6 ARG
Chi-restraints excluded: chain B residue   32 MET
Chi-restraints excluded: chain B residue   37 LYS
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  232 THR
Chi-restraints excluded: chain B residue  247 ILE
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  402 HIS
Chi-restraints excluded: chain C residue  420 ILE
Chi-restraints excluded: chain C residue  422 TYR
Chi-restraints excluded: chain C residue  426 VAL
Chi-restraints excluded: chain C residue  441 VAL
Chi-restraints excluded: chain C residue  517 PHE
Chi-restraints excluded: chain C residue  518 VAL
Chi-restraints excluded: chain C residue  564 SER
Chi-restraints excluded: chain D residue  445 TRP
Chi-restraints excluded: chain D residue  447 MET
Chi-restraints excluded: chain D residue  468 VAL
Chi-restraints excluded: chain D residue  483 ILE
Chi-restraints excluded: chain D residue  496 TYR
Chi-restraints excluded: chain D residue  499 LEU
Chi-restraints excluded: chain D residue  518 VAL
Chi-restraints excluded: chain D residue  520 THR
Chi-restraints excluded: chain D residue  558 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 88 optimal weight:    0.0040
   chunk 56 optimal weight:    0.4980
   chunk 124 optimal weight:    3.9990
   chunk 104 optimal weight:    3.9990
   chunk 85 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 52 optimal weight:    0.8980
   chunk 102 optimal weight:    0.6980
   overall best weight:    0.5992

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

Flipped N/Q/H residues before XYZ refinement:
** B   5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.126273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.093519 restraints weight = 22556.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.096084 restraints weight = 14853.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.097777 restraints weight = 11264.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10564  Z= 0.184
  Angle     :  0.585  10.026  14240  Z= 0.294
  Chirality :  0.041   0.138   1540
  Planarity :  0.003   0.036   1822
  Dihedral  :  4.481  32.522   1396
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 34.12 %
    Favored  : 61.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.04 (0.24), residues: 1276
  helix:  0.75 (0.24), residues: 508
  sheet: -1.91 (0.45), residues: 144
  loop : -1.63 (0.25), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D 584 
 HIS   0.008   0.001   HIS B 288 
 PHE   0.018   0.001   PHE D 517 
 TYR   0.014   0.001   TYR A 334 
 ARG   0.003   0.000   ARG C 438 

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 156
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.8107 (t80)
REVERT: A  229 MET cc_start: 0.9124 (pmm) cc_final: 0.8554 (pmm)
REVERT: A  292 MET cc_start: 0.8783 (mmm) cc_final: 0.8553 (mmm)
REVERT: A  387 MET cc_start: 0.8810 (pmm) cc_final: 0.8469 (pmm)
REVERT: A  404 THR cc_start: 0.7715 (m) cc_final: 0.7078 (p)
REVERT: B   37 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8775 (mtmm)
REVERT: B   95 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8126 (t80)
REVERT: B  292 MET cc_start: 0.7496 (mtm) cc_final: 0.7243 (mtm)
REVERT: C  422 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7402 (t80)
REVERT: C  484 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.8026 (mtp)
REVERT: C  590 MET cc_start: 0.8107 (tmm) cc_final: 0.7762 (mmm)
REVERT: D  438 ARG cc_start: 0.8564 (tmm160) cc_final: 0.8249 (ttp80)
REVERT: D  496 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.8114 (m-80)
REVERT: D  510 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7794 (t80)
  outliers start: 46
  outliers final: 34
  residues processed: 185
  average time/residue: 0.2142
  time to fit residues: 57.1982
Evaluate side-chains
  188 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 147
  time to evaluate  : 1.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 TYR
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  205 ARG
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain B residue    6 ARG
Chi-restraints excluded: chain B residue   32 MET
Chi-restraints excluded: chain B residue   37 LYS
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  232 THR
Chi-restraints excluded: chain B residue  247 ILE
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain C residue  420 ILE
Chi-restraints excluded: chain C residue  422 TYR
Chi-restraints excluded: chain C residue  426 VAL
Chi-restraints excluded: chain C residue  484 MET
Chi-restraints excluded: chain C residue  517 PHE
Chi-restraints excluded: chain C residue  518 VAL
Chi-restraints excluded: chain C residue  564 SER
Chi-restraints excluded: chain D residue  445 TRP
Chi-restraints excluded: chain D residue  447 MET
Chi-restraints excluded: chain D residue  468 VAL
Chi-restraints excluded: chain D residue  483 ILE
Chi-restraints excluded: chain D residue  496 TYR
Chi-restraints excluded: chain D residue  510 PHE
Chi-restraints excluded: chain D residue  518 VAL
Chi-restraints excluded: chain D residue  520 THR
Chi-restraints excluded: chain D residue  558 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 65 optimal weight:    0.2980
   chunk 21 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 19 optimal weight:    0.2980
   chunk 45 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   chunk 77 optimal weight:    0.5980
   chunk 113 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** B   5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 402 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.127412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.093925 restraints weight = 22570.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.096492 restraints weight = 14602.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.098200 restraints weight = 11079.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10564  Z= 0.182
  Angle     :  0.592  10.056  14240  Z= 0.296
  Chirality :  0.041   0.139   1540
  Planarity :  0.003   0.036   1822
  Dihedral  :  4.443  32.080   1396
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 34.39 %
    Favored  : 61.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.07 (0.24), residues: 1276
  helix:  0.71 (0.24), residues: 518
  sheet: -2.01 (0.45), residues: 148
  loop : -1.63 (0.26), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP D 584 
 HIS   0.010   0.001   HIS B 288 
 PHE   0.021   0.001   PHE C 502 
 TYR   0.015   0.001   TYR B 388 
 ARG   0.004   0.000   ARG B 226 

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 160
  time to evaluate  : 1.389 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8093 (t80)
REVERT: A  229 MET cc_start: 0.9129 (pmm) cc_final: 0.8615 (pmm)
REVERT: A  292 MET cc_start: 0.8730 (mmm) cc_final: 0.8530 (mmm)
REVERT: A  387 MET cc_start: 0.8793 (pmm) cc_final: 0.8571 (pmm)
REVERT: A  398 MET cc_start: 0.7647 (mmp) cc_final: 0.7204 (mmm)
REVERT: B   37 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8743 (mtmm)
REVERT: B   95 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8089 (t80)
REVERT: B  231 ILE cc_start: 0.8804 (mm) cc_final: 0.8558 (mm)
REVERT: B  292 MET cc_start: 0.7464 (mtm) cc_final: 0.7192 (mtm)
REVERT: B  402 HIS cc_start: 0.8547 (OUTLIER) cc_final: 0.8291 (t70)
REVERT: C  422 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.7421 (t80)
REVERT: C  484 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7992 (mtp)
REVERT: C  590 MET cc_start: 0.8186 (tmm) cc_final: 0.7748 (mmm)
REVERT: D  496 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.8179 (m-80)
REVERT: D  510 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7776 (t80)
REVERT: D  592 MET cc_start: 0.5285 (pmm) cc_final: 0.4788 (pmm)
  outliers start: 48
  outliers final: 35
  residues processed: 190
  average time/residue: 0.2192
  time to fit residues: 59.5143
Evaluate side-chains
  192 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 149
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 TYR
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  205 ARG
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain B residue    6 ARG
Chi-restraints excluded: chain B residue   32 MET
Chi-restraints excluded: chain B residue   37 LYS
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  232 THR
Chi-restraints excluded: chain B residue  247 ILE
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  391 TYR
Chi-restraints excluded: chain B residue  402 HIS
Chi-restraints excluded: chain C residue  420 ILE
Chi-restraints excluded: chain C residue  422 TYR
Chi-restraints excluded: chain C residue  426 VAL
Chi-restraints excluded: chain C residue  484 MET
Chi-restraints excluded: chain C residue  517 PHE
Chi-restraints excluded: chain C residue  518 VAL
Chi-restraints excluded: chain C residue  564 SER
Chi-restraints excluded: chain D residue  445 TRP
Chi-restraints excluded: chain D residue  447 MET
Chi-restraints excluded: chain D residue  468 VAL
Chi-restraints excluded: chain D residue  483 ILE
Chi-restraints excluded: chain D residue  496 TYR
Chi-restraints excluded: chain D residue  499 LEU
Chi-restraints excluded: chain D residue  510 PHE
Chi-restraints excluded: chain D residue  518 VAL
Chi-restraints excluded: chain D residue  520 THR
Chi-restraints excluded: chain D residue  558 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 22 optimal weight:    3.9990
   chunk 118 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   chunk 39 optimal weight:    0.3980
   chunk 35 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B   5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 402 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.127134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.096533 restraints weight = 22388.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.097609 restraints weight = 14056.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.098398 restraints weight = 10742.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.2291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10564  Z= 0.196
  Angle     :  0.612  12.014  14240  Z= 0.306
  Chirality :  0.041   0.156   1540
  Planarity :  0.003   0.036   1822
  Dihedral  :  4.536  43.863   1396
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 35.02 %
    Favored  : 60.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.09 (0.24), residues: 1276
  helix:  0.70 (0.24), residues: 518
  sheet: -1.82 (0.50), residues: 128
  loop : -1.73 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 259 
 HIS   0.009   0.001   HIS B 288 
 PHE   0.017   0.001   PHE D 517 
 TYR   0.018   0.001   TYR B 334 
 ARG   0.003   0.000   ARG B 226 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3082.96 seconds
wall clock time: 56 minutes 40.41 seconds (3400.41 seconds total)