Starting phenix.real_space_refine
on Wed Mar 12 16:36:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ozm_17314/03_2025/8ozm_17314.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ozm_17314/03_2025/8ozm_17314.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ozm_17314/03_2025/8ozm_17314.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ozm_17314/03_2025/8ozm_17314.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ozm_17314/03_2025/8ozm_17314.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ozm_17314/03_2025/8ozm_17314.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      30      5.16       5
     C    5088      2.51       5
     N    1452      2.21       5
     O    1482      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8052
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1342
          Classifications: {'peptide': 175}
          Link IDs: {'PTRANS': 11, 'TRANS': 163}
    Chain: "C"
      Number of atoms: 1342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1342
          Classifications: {'peptide': 175}
          Link IDs: {'PTRANS': 11, 'TRANS': 163}
    Chain: "D"
      Number of atoms: 1342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1342
          Classifications: {'peptide': 175}
          Link IDs: {'PTRANS': 11, 'TRANS': 163}
    Chain: "E"
      Number of atoms: 1342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1342
          Classifications: {'peptide': 175}
          Link IDs: {'PTRANS': 11, 'TRANS': 163}
    Chain: "F"
      Number of atoms: 1342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1342
          Classifications: {'peptide': 175}
          Link IDs: {'PTRANS': 11, 'TRANS': 163}
    Chain: "G"
      Number of atoms: 1342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1342
          Classifications: {'peptide': 175}
          Link IDs: {'PTRANS': 11, 'TRANS': 163}
  Time building chain proxies: 5.95, per 1000 atoms: 0.74
  Number of scatterers: 8052
  At special positions: 0
  Unit cell: (117.72, 124.2, 84.24, 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      30     16.00
     O    1482      8.00
     N    1452      7.00
     C    5088      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: 1.90
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1884

  Finding SS restraints...
    Secondary structure from input PDB file:
      73 helices and 0 sheets defined
      77.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'B' and resid 306 through 315
      removed outlier: 3.836A  pdb=" N   SER B 312 " --> pdb=" O   GLN B 308 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   THR B 314 " --> pdb=" O   ILE B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 330
    Processing helix  chain 'B' and resid 331 through 339
      removed outlier: 3.601A  pdb=" N   GLY B 337 " --> pdb=" O   PRO B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 343 through 356
      removed outlier: 3.527A  pdb=" N   GLY B 356 " --> pdb=" O   ASN B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 384
      removed outlier: 3.755A  pdb=" N   THR B 382 " --> pdb=" O   LEU B 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 389
      removed outlier: 3.694A  pdb=" N   HIS B 389 " --> pdb=" O   PHE B 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 386 through 389'
    Processing helix  chain 'B' and resid 390 through 402
      removed outlier: 3.683A  pdb=" N   GLN B 401 " --> pdb=" O   GLY B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 416
      removed outlier: 3.531A  pdb=" N   THR B 409 " --> pdb=" O   ALA B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 430
      removed outlier: 3.803A  pdb=" N   GLY B 428 " --> pdb=" O   GLY B 424 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   TYR B 429 " --> pdb=" O   ILE B 425 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 444
      removed outlier: 3.520A  pdb=" N   VAL B 436 " --> pdb=" O   GLY B 432 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ARG B 442 " --> pdb=" O   ALA B 438 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 453
    Processing helix  chain 'B' and resid 455 through 468
      removed outlier: 3.532A  pdb=" N   LEU B 467 " --> pdb=" O   VAL B 463 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 306 through 314
    Processing helix  chain 'C' and resid 323 through 331
      removed outlier: 3.778A  pdb=" N   GLY C 329 " --> pdb=" O   PRO C 325 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 331 through 339
      removed outlier: 3.520A  pdb=" N   ILE C 335 " --> pdb=" O   ASN C 331 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 343 through 356
    Processing helix  chain 'C' and resid 364 through 368
    Processing helix  chain 'C' and resid 370 through 384
    Processing helix  chain 'C' and resid 387 through 389
      No H-bonds generated for 'chain 'C' and resid 387 through 389'
    Processing helix  chain 'C' and resid 390 through 402
      removed outlier: 3.506A  pdb=" N   VAL C 394 " --> pdb=" O   GLN C 390 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLN C 401 " --> pdb=" O   GLY C 397 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 403 through 412
    Processing helix  chain 'C' and resid 418 through 427
    Processing helix  chain 'C' and resid 432 through 445
      removed outlier: 3.523A  pdb=" N   VAL C 436 " --> pdb=" O   GLY C 432 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ARG C 442 " --> pdb=" O   ALA C 438 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 448 through 455
    Processing helix  chain 'C' and resid 455 through 467
    Processing helix  chain 'D' and resid 306 through 315
      removed outlier: 3.627A  pdb=" N   ILE D 310 " --> pdb=" O   PRO D 306 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 320 through 322
      No H-bonds generated for 'chain 'D' and resid 320 through 322'
    Processing helix  chain 'D' and resid 323 through 331
      removed outlier: 3.651A  pdb=" N   TRP D 327 " --> pdb=" O   GLU D 323 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 331 through 339
    Processing helix  chain 'D' and resid 343 through 356
      removed outlier: 3.686A  pdb=" N   ARG D 347 " --> pdb=" O   THR D 343 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 364 through 368
    Processing helix  chain 'D' and resid 370 through 384
      removed outlier: 3.595A  pdb=" N   VAL D 375 " --> pdb=" O   TRP D 371 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 387 through 402
      removed outlier: 3.511A  pdb=" N   ASP D 400 " --> pdb=" O   LYS D 396 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 403 through 415
      removed outlier: 3.614A  pdb=" N   THR D 409 " --> pdb=" O   ALA D 405 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 418 through 427
      removed outlier: 3.530A  pdb=" N   GLY D 424 " --> pdb=" O   GLN D 420 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 432 through 446
      removed outlier: 3.644A  pdb=" N   VAL D 436 " --> pdb=" O   GLY D 432 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ARG D 442 " --> pdb=" O   ALA D 438 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   GLN D 445 " --> pdb=" O   GLN D 441 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLU D 446 " --> pdb=" O   ARG D 442 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 448 through 455
    Processing helix  chain 'D' and resid 455 through 467
      removed outlier: 3.618A  pdb=" N   HIS D 459 " --> pdb=" O   THR D 455 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 306 through 315
      removed outlier: 3.542A  pdb=" N   VAL E 313 " --> pdb=" O   HIS E 309 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 320 through 322
      No H-bonds generated for 'chain 'E' and resid 320 through 322'
    Processing helix  chain 'E' and resid 323 through 339
      removed outlier: 3.567A  pdb=" N   TRP E 327 " --> pdb=" O   GLU E 323 " (cutoff:3.500A)
      Proline residue:  E 333  - end of helix
    Processing helix  chain 'E' and resid 343 through 356
    Processing helix  chain 'E' and resid 364 through 368
    Processing helix  chain 'E' and resid 370 through 384
      removed outlier: 3.650A  pdb=" N   THR E 382 " --> pdb=" O   LEU E 378 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 387 through 403
      removed outlier: 3.770A  pdb=" N   ASN E 393 " --> pdb=" O   HIS E 389 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLN E 401 " --> pdb=" O   GLY E 397 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 403 through 415
      removed outlier: 3.563A  pdb=" N   ALA E 407 " --> pdb=" O   GLY E 403 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER E 415 " --> pdb=" O   GLY E 411 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 418 through 428
      removed outlier: 4.126A  pdb=" N   GLY E 428 " --> pdb=" O   GLY E 424 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 432 through 445
      removed outlier: 3.703A  pdb=" N   VAL E 436 " --> pdb=" O   GLY E 432 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 448 through 455
    Processing helix  chain 'E' and resid 455 through 468
    Processing helix  chain 'F' and resid 306 through 315
      removed outlier: 3.582A  pdb=" N   ILE F 310 " --> pdb=" O   PRO F 306 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   SER F 312 " --> pdb=" O   GLN F 308 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 323 through 339
      removed outlier: 3.717A  pdb=" N   GLY F 329 " --> pdb=" O   PRO F 325 " (cutoff:3.500A)
      Proline residue:  F 333  - end of helix
      removed outlier: 3.579A  pdb=" N   GLY F 337 " --> pdb=" O   PRO F 333 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 343 through 356
    Processing helix  chain 'F' and resid 370 through 384
    Processing helix  chain 'F' and resid 386 through 389
    Processing helix  chain 'F' and resid 390 through 400
      removed outlier: 3.870A  pdb=" N   GLY F 397 " --> pdb=" O   ASN F 393 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 403 through 416
    Processing helix  chain 'F' and resid 418 through 427
    Processing helix  chain 'F' and resid 428 through 430
      No H-bonds generated for 'chain 'F' and resid 428 through 430'
    Processing helix  chain 'F' and resid 432 through 446
      removed outlier: 3.747A  pdb=" N   ARG F 442 " --> pdb=" O   ALA F 438 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ASP F 444 " --> pdb=" O   GLN F 440 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLU F 446 " --> pdb=" O   ARG F 442 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 448 through 468
      removed outlier: 5.801A  pdb=" N   ILE F 457 " --> pdb=" O   ALA F 453 " (cutoff:3.500A)
      removed outlier: 5.188A  pdb=" N   GLN F 458 " --> pdb=" O   GLU F 454 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA F 462 " --> pdb=" O   GLN F 458 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 306 through 315
    Processing helix  chain 'G' and resid 323 through 331
      removed outlier: 3.553A  pdb=" N   GLY G 329 " --> pdb=" O   PRO G 325 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 331 through 339
    Processing helix  chain 'G' and resid 343 through 355
    Processing helix  chain 'G' and resid 358 through 362
      removed outlier: 3.792A  pdb=" N   SER G 362 " --> pdb=" O   ILE G 359 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 370 through 384
    Processing helix  chain 'G' and resid 387 through 389
      No H-bonds generated for 'chain 'G' and resid 387 through 389'
    Processing helix  chain 'G' and resid 390 through 402
      removed outlier: 3.504A  pdb=" N   GLY G 397 " --> pdb=" O   ASN G 393 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 403 through 415
    Processing helix  chain 'G' and resid 418 through 429
      removed outlier: 3.902A  pdb=" N   VAL G 422 " --> pdb=" O   ASN G 418 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   GLY G 428 " --> pdb=" O   GLY G 424 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   TYR G 429 " --> pdb=" O   ILE G 425 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 432 through 445
      removed outlier: 3.560A  pdb=" N   VAL G 436 " --> pdb=" O   GLY G 432 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ARG G 442 " --> pdb=" O   ALA G 438 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 448 through 468
      removed outlier: 3.506A  pdb=" N   GLU G 454 " --> pdb=" O   GLN G 450 " (cutoff:3.500A)
      removed outlier: 5.691A  pdb=" N   ILE G 457 " --> pdb=" O   ALA G 453 " (cutoff:3.500A)
      removed outlier: 4.816A  pdb=" N   GLN G 458 " --> pdb=" O   GLU G 454 " (cutoff:3.500A)

    468 hydrogen bonds defined for protein.
    1380 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.97

  Time building geometry restraints manager: 2.28 seconds

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

  Histogram of bond lengths:
        1.18 -     1.32: 1413
        1.32 -     1.45: 2011
        1.45 -     1.59: 4736
        1.59 -     1.72: 0
        1.72 -     1.86: 48
  Bond restraints: 8208
  Sorted by residual:
  bond pdb=" N   ILE G 305 "
       pdb=" CA  ILE G 305 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.036 7.30e-03 1.88e+04 2.48e+01
  bond pdb=" N   PHE E 386 "
       pdb=" CA  PHE E 386 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 7.40e-03 1.83e+04 2.23e+01
  bond pdb=" N   MET E 413 "
       pdb=" CA  MET E 413 "
    ideal  model  delta    sigma   weight residual
    1.459  1.510 -0.052 1.16e-02 7.43e+03 1.98e+01
  bond pdb=" C   ASP C 345 "
       pdb=" O   ASP C 345 "
    ideal  model  delta    sigma   weight residual
    1.236  1.287 -0.051 1.16e-02 7.43e+03 1.92e+01
  bond pdb=" N   VAL B 404 "
       pdb=" CA  VAL B 404 "
    ideal  model  delta    sigma   weight residual
    1.460  1.509 -0.049 1.19e-02 7.06e+03 1.72e+01
  ... (remaining 8203 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 9118
        2.57 -     5.15: 1972
        5.15 -     7.72: 102
        7.72 -    10.29: 3
       10.29 -    12.86: 1
  Bond angle restraints: 11196
  Sorted by residual:
  angle pdb=" CA  GLY G 384 "
        pdb=" C   GLY G 384 "
        pdb=" O   GLY G 384 "
      ideal   model   delta    sigma   weight residual
     122.22  118.38    3.84 6.50e-01 2.37e+00 3.48e+01
  angle pdb=" CG  ARG E 381 "
        pdb=" CD  ARG E 381 "
        pdb=" NE  ARG E 381 "
      ideal   model   delta    sigma   weight residual
     112.00   99.14   12.86 2.20e+00 2.07e-01 3.42e+01
  angle pdb=" C   ILE C 359 "
        pdb=" N   GLY C 360 "
        pdb=" CA  GLY C 360 "
      ideal   model   delta    sigma   weight residual
     119.99  126.46   -6.47 1.13e+00 7.83e-01 3.28e+01
  angle pdb=" N   PRO F 431 "
        pdb=" CA  PRO F 431 "
        pdb=" CB  PRO F 431 "
      ideal   model   delta    sigma   weight residual
     102.28   98.07    4.21 7.50e-01 1.78e+00 3.15e+01
  angle pdb=" N   ILE D 351 "
        pdb=" CA  ILE D 351 "
        pdb=" C   ILE D 351 "
      ideal   model   delta    sigma   weight residual
     110.30  104.88    5.42 9.70e-01 1.06e+00 3.13e+01
  ... (remaining 11191 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.60: 4243
       15.60 -    31.20: 507
       31.20 -    46.81: 108
       46.81 -    62.41: 37
       62.41 -    78.01: 13
  Dihedral angle restraints: 4908
    sinusoidal: 1956
      harmonic: 2952
  Sorted by residual:
  dihedral pdb=" CA  LEU F 355 "
           pdb=" C   LEU F 355 "
           pdb=" N   GLY F 356 "
           pdb=" CA  GLY F 356 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.27   26.73     0      5.00e+00 4.00e-02 2.86e+01
  dihedral pdb=" CA  GLU D 446 "
           pdb=" C   GLU D 446 "
           pdb=" N   ILE D 447 "
           pdb=" CA  ILE D 447 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.55  -24.45     0      5.00e+00 4.00e-02 2.39e+01
  dihedral pdb=" CA  PRO E 387 "
           pdb=" C   PRO E 387 "
           pdb=" N   MET E 388 "
           pdb=" CA  MET E 388 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.59  -23.41     0      5.00e+00 4.00e-02 2.19e+01
  ... (remaining 4905 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 609
       0.060 -    0.120: 464
       0.120 -    0.179: 188
       0.179 -    0.239: 39
       0.239 -    0.299: 14
  Chirality restraints: 1314
  Sorted by residual:
  chirality pdb=" CB  VAL G 399 "
            pdb=" CA  VAL G 399 "
            pdb=" CG1 VAL G 399 "
            pdb=" CG2 VAL G 399 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.24e+00
  chirality pdb=" CA  VAL G 341 "
            pdb=" N   VAL G 341 "
            pdb=" C   VAL G 341 "
            pdb=" CB  VAL G 341 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.74   -0.29 2.00e-01 2.50e+01 2.16e+00
  chirality pdb=" CB  VAL B 338 "
            pdb=" CA  VAL B 338 "
            pdb=" CG1 VAL B 338 "
            pdb=" CG2 VAL B 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.99e+00
  ... (remaining 1311 not shown)

  Planarity restraints: 1470
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 408 "    0.044 2.00e-02 2.50e+03   2.28e-02 1.04e+01
        pdb=" CG  TYR F 408 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 408 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 408 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 408 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 408 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 408 "    0.007 2.00e-02 2.50e+03
        pdb=" OH  TYR F 408 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B 390 "    0.013 2.00e-02 2.50e+03   2.73e-02 7.46e+00
        pdb=" C   GLN B 390 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   GLN B 390 "    0.018 2.00e-02 2.50e+03
        pdb=" N   LEU B 391 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 408 "    0.009 2.00e-02 2.50e+03   1.87e-02 7.02e+00
        pdb=" CG  TYR D 408 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 408 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 408 "    0.019 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 408 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 408 "   -0.024 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 408 "   -0.025 2.00e-02 2.50e+03
        pdb=" OH  TYR D 408 "    0.033 2.00e-02 2.50e+03
  ... (remaining 1467 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.89: 2485
        2.89 -     3.39: 8040
        3.39 -     3.89: 12633
        3.89 -     4.40: 14552
        4.40 -     4.90: 23656
  Nonbonded interactions: 61366
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN F 440 "
            pdb=" OD1 ASP F 444 "
     model   vdw
     2.384 3.120
  nonbonded pdb=" O   HIS E 309 "
            pdb=" OG  SER E 312 "
     model   vdw
     2.392 3.040
  nonbonded pdb=" O   HIS G 309 "
            pdb=" OG  SER G 312 "
     model   vdw
     2.421 3.040
  nonbonded pdb=" NH1 ARG E 311 "
            pdb=" OE2 GLU E 316 "
     model   vdw
     2.466 3.120
  nonbonded pdb=" O   GLN F 390 "
            pdb=" N   ASN F 393 "
     model   vdw
     2.472 3.120
  ... (remaining 61361 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

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 individual isotropic
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:             2.070
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.170
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
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      :  0.015   0.060   8208  Z= 0.964
  Angle     :  1.933  12.862  11196  Z= 1.440
  Chirality :  0.091   0.299   1314
  Planarity :  0.006   0.043   1470
  Dihedral  : 15.029  78.012   3024
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  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: -4.75 (0.19), residues: 1038
  helix: -2.96 (0.14), residues: 710
  sheet:  None (None), residues: 0
  loop : -3.15 (0.27), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.008   TRP E 327 
 HIS   0.017   0.004   HIS F 389 
 PHE   0.031   0.007   PHE E 386 
 TYR   0.044   0.010   TYR F 408 
 ARG   0.042   0.002   ARG E 311 

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.894 
Fit side-chains
REVERT: B  358 ASN cc_start: 0.6732 (m-40) cc_final: 0.6232 (m110)
REVERT: B  381 ARG cc_start: 0.7513 (mtt180) cc_final: 0.7298 (mmt90)
REVERT: B  472 ARG cc_start: 0.7974 (ttt180) cc_final: 0.7769 (ttm-80)
REVERT: C  319 ARG cc_start: 0.7800 (mtt180) cc_final: 0.7468 (mtm180)
REVERT: C  322 ARG cc_start: 0.7163 (mtt180) cc_final: 0.6933 (mmm-85)
REVERT: D  429 TYR cc_start: 0.8357 (m-80) cc_final: 0.8143 (m-80)
REVERT: D  450 GLN cc_start: 0.7588 (mt0) cc_final: 0.7373 (tp40)
REVERT: E  308 GLN cc_start: 0.7610 (tt0) cc_final: 0.7060 (tt0)
REVERT: E  415 SER cc_start: 0.8333 (t) cc_final: 0.7980 (t)
REVERT: E  450 GLN cc_start: 0.7137 (tt0) cc_final: 0.6857 (tp-100)
REVERT: F  402 GLU cc_start: 0.8044 (mp0) cc_final: 0.7693 (mm-30)
REVERT: G  319 ARG cc_start: 0.8292 (mtt-85) cc_final: 0.8013 (mtm180)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.2593
  time to fit residues: 54.9312
Evaluate side-chains
  134 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 79 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0970
   chunk 48 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0170
   chunk 92 optimal weight:    0.5980
   overall best weight:    0.4616

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

Flipped N/Q/H residues before XYZ refinement:
B 320 ASN
B 440 GLN
B 441 GLN
** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 440 GLN
C 441 GLN
D 440 GLN
D 461 ASN
F 389 HIS
G 308 GLN
G 441 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.098271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.084345 restraints weight = 11021.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.2743 rms_B_bonded: 1.62
r_work: 0.2612 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2475 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8208  Z= 0.195
  Angle     :  0.642   6.116  11196  Z= 0.333
  Chirality :  0.042   0.204   1314
  Planarity :  0.005   0.042   1470
  Dihedral  :  4.827  19.123   1140
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 10.11 %
    Favored  : 88.39 %
  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: -1.04 (0.24), residues: 1038
  helix: -0.12 (0.18), residues: 754
  sheet:  None (None), residues: 0
  loop : -2.02 (0.31), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP F 327 
 HIS   0.007   0.001   HIS G 389 
 PHE   0.012   0.001   PHE E 379 
 TYR   0.010   0.001   TYR E 419 
 ARG   0.004   0.001   ARG E 322 

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 145
  time to evaluate  : 0.867 
Fit side-chains
REVERT: B  358 ASN cc_start: 0.8001 (m-40) cc_final: 0.7655 (m-40)
REVERT: C  319 ARG cc_start: 0.7820 (mtt180) cc_final: 0.7426 (mtm180)
REVERT: C  322 ARG cc_start: 0.8640 (mtt180) cc_final: 0.8251 (mmm-85)
REVERT: C  440 GLN cc_start: 0.8495 (tp40) cc_final: 0.8042 (tp40)
REVERT: C  441 GLN cc_start: 0.8261 (mt0) cc_final: 0.7983 (tp40)
REVERT: C  444 ASP cc_start: 0.8070 (m-30) cc_final: 0.7583 (m-30)
REVERT: D  429 TYR cc_start: 0.9082 (m-80) cc_final: 0.8877 (m-80)
REVERT: D  447 ILE cc_start: 0.8340 (tp) cc_final: 0.8079 (tp)
REVERT: E  401 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7939 (mm110)
REVERT: F  402 GLU cc_start: 0.8563 (mp0) cc_final: 0.8127 (mm-30)
REVERT: F  412 MET cc_start: 0.9020 (mmm) cc_final: 0.8768 (mmt)
REVERT: G  319 ARG cc_start: 0.8496 (mtt-85) cc_final: 0.8186 (mtm180)
  outliers start: 13
  outliers final: 6
  residues processed: 152
  average time/residue: 0.2490
  time to fit residues: 48.3789
Evaluate side-chains
  120 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 114
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain D residue  369 LEU
Chi-restraints excluded: chain D residue  380 ILE
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain F residue  364 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 64 optimal weight:    0.0370
   chunk 97 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 100 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 69 optimal weight:    0.0170
   chunk 23 optimal weight:    0.0040
   chunk 22 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.3708

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

Flipped N/Q/H residues before XYZ refinement:
C 331 ASN
E 441 GLN
E 445 GLN
F 440 GLN
G 420 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.100505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.086573 restraints weight = 11098.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.2778 rms_B_bonded: 1.62
r_work: 0.2648 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2513 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8208  Z= 0.149
  Angle     :  0.517   5.766  11196  Z= 0.262
  Chirality :  0.039   0.137   1314
  Planarity :  0.004   0.036   1470
  Dihedral  :  4.039  14.766   1140
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 11.38 %
    Favored  : 86.78 %
  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:  0.69 (0.26), residues: 1038
  helix:  1.10 (0.19), residues: 782
  sheet:  None (None), residues: 0
  loop : -1.49 (0.35), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 327 
 HIS   0.004   0.001   HIS G 389 
 PHE   0.004   0.001   PHE C 379 
 TYR   0.007   0.001   TYR D 464 
 ARG   0.005   0.000   ARG C 452 

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.870 
Fit side-chains
REVERT: B  358 ASN cc_start: 0.7944 (m-40) cc_final: 0.7566 (m-40)
REVERT: B  420 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8154 (mp10)
REVERT: C  319 ARG cc_start: 0.7824 (mtt180) cc_final: 0.7487 (mtm180)
REVERT: C  322 ARG cc_start: 0.8637 (mtt180) cc_final: 0.8295 (mmm-85)
REVERT: D  312 SER cc_start: 0.9000 (OUTLIER) cc_final: 0.8641 (p)
REVERT: F  402 GLU cc_start: 0.8443 (mp0) cc_final: 0.8134 (mm-30)
REVERT: F  412 MET cc_start: 0.8992 (mmm) cc_final: 0.8688 (mmt)
REVERT: G  319 ARG cc_start: 0.8410 (mtt-85) cc_final: 0.8175 (mtm180)
REVERT: G  465 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8337 (mt-10)
  outliers start: 16
  outliers final: 7
  residues processed: 130
  average time/residue: 0.2107
  time to fit residues: 36.9530
Evaluate side-chains
  116 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  312 SER
Chi-restraints excluded: chain D residue  369 LEU
Chi-restraints excluded: chain D residue  454 GLU
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain F residue  336 ASP
Chi-restraints excluded: chain F residue  364 THR
Chi-restraints excluded: chain F residue  475 SER
Chi-restraints excluded: chain G residue  423 SER
Chi-restraints excluded: chain G residue  465 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 87 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 99 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 69 optimal weight:    0.2980
   chunk 100 optimal weight:    0.9980
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
C 308 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.096242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.083054 restraints weight = 11172.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.2722 rms_B_bonded: 1.53
r_work: 0.2591 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2459 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.2982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8208  Z= 0.258
  Angle     :  0.551   5.840  11196  Z= 0.278
  Chirality :  0.042   0.165   1314
  Planarity :  0.004   0.037   1470
  Dihedral  :  3.915  15.377   1140
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 11.84 %
    Favored  : 85.63 %
  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:  0.97 (0.26), residues: 1038
  helix:  1.36 (0.19), residues: 766
  sheet:  None (None), residues: 0
  loop : -1.39 (0.35), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 327 
 HIS   0.006   0.001   HIS F 389 
 PHE   0.010   0.001   PHE B 456 
 TYR   0.009   0.001   TYR C 464 
 ARG   0.005   0.000   ARG G 472 

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.882 
Fit side-chains
REVERT: B  358 ASN cc_start: 0.7846 (m-40) cc_final: 0.7322 (m-40)
REVERT: C  319 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7481 (mtm180)
REVERT: C  322 ARG cc_start: 0.8665 (mtt180) cc_final: 0.8327 (mmm-85)
REVERT: D  396 LYS cc_start: 0.8753 (tttt) cc_final: 0.8497 (tttp)
REVERT: F  402 GLU cc_start: 0.8455 (mp0) cc_final: 0.8110 (mm-30)
REVERT: F  412 MET cc_start: 0.9069 (mmm) cc_final: 0.8693 (mmt)
REVERT: G  319 ARG cc_start: 0.8427 (mtt-85) cc_final: 0.8189 (mtm180)
REVERT: G  450 GLN cc_start: 0.7540 (tp40) cc_final: 0.7262 (tp40)
REVERT: G  465 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8286 (mt-10)
  outliers start: 22
  outliers final: 14
  residues processed: 131
  average time/residue: 0.2125
  time to fit residues: 37.3854
Evaluate side-chains
  126 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  400 ASP
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain D residue  369 LEU
Chi-restraints excluded: chain D residue  380 ILE
Chi-restraints excluded: chain D residue  454 GLU
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain F residue  336 ASP
Chi-restraints excluded: chain F residue  364 THR
Chi-restraints excluded: chain F residue  415 SER
Chi-restraints excluded: chain F residue  465 GLU
Chi-restraints excluded: chain F residue  475 SER
Chi-restraints excluded: chain G residue  370 THR
Chi-restraints excluded: chain G residue  423 SER
Chi-restraints excluded: chain G residue  465 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 92 optimal weight:    4.9990
   chunk 95 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.2984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.097566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.084023 restraints weight = 11027.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.2737 rms_B_bonded: 1.58
r_work: 0.2608 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2476 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8208  Z= 0.210
  Angle     :  0.511   5.650  11196  Z= 0.258
  Chirality :  0.040   0.165   1314
  Planarity :  0.004   0.035   1470
  Dihedral  :  3.748  14.156   1140
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 12.30 %
    Favored  : 85.40 %
  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:  1.28 (0.26), residues: 1038
  helix:  1.60 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop : -1.20 (0.35), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 327 
 HIS   0.005   0.001   HIS F 389 
 PHE   0.006   0.001   PHE F 339 
 TYR   0.007   0.001   TYR C 464 
 ARG   0.005   0.000   ARG G 472 

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.874 
Fit side-chains
REVERT: B  319 ARG cc_start: 0.7393 (ptp-170) cc_final: 0.7062 (mtm-85)
REVERT: B  358 ASN cc_start: 0.7733 (m-40) cc_final: 0.7180 (m-40)
REVERT: B  420 GLN cc_start: 0.8350 (mm-40) cc_final: 0.7980 (mp10)
REVERT: C  319 ARG cc_start: 0.7894 (mtt180) cc_final: 0.7433 (mtm180)
REVERT: C  322 ARG cc_start: 0.8669 (mtt180) cc_final: 0.8308 (mmm-85)
REVERT: D  396 LYS cc_start: 0.8677 (tttt) cc_final: 0.8466 (tttp)
REVERT: F  402 GLU cc_start: 0.8393 (mp0) cc_final: 0.8067 (mm-30)
REVERT: F  412 MET cc_start: 0.9043 (mmm) cc_final: 0.8587 (mmt)
REVERT: G  319 ARG cc_start: 0.8488 (mtt-85) cc_final: 0.8144 (mtm180)
  outliers start: 20
  outliers final: 11
  residues processed: 118
  average time/residue: 0.2165
  time to fit residues: 34.4587
Evaluate side-chains
  116 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain C residue  476 ILE
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain D residue  369 LEU
Chi-restraints excluded: chain D residue  454 GLU
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain F residue  336 ASP
Chi-restraints excluded: chain F residue  364 THR
Chi-restraints excluded: chain F residue  466 ILE
Chi-restraints excluded: chain F residue  475 SER
Chi-restraints excluded: chain G residue  423 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 16 optimal weight:    0.4980
   chunk 94 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 88 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0970
   chunk 17 optimal weight:    0.9990
   chunk 101 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 389 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.100146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.086484 restraints weight = 11098.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.2776 rms_B_bonded: 1.61
r_work: 0.2647 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2514 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.3485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8208  Z= 0.148
  Angle     :  0.472   5.548  11196  Z= 0.238
  Chirality :  0.039   0.131   1314
  Planarity :  0.004   0.034   1470
  Dihedral  :  3.519  12.221   1140
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 1.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.87 %
    Favored  : 85.52 %
  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:  1.64 (0.27), residues: 1038
  helix:  1.81 (0.19), residues: 766
  sheet:  None (None), residues: 0
  loop : -1.00 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 327 
 HIS   0.003   0.001   HIS G 389 
 PHE   0.004   0.001   PHE D 456 
 TYR   0.005   0.001   TYR C 464 
 ARG   0.004   0.000   ARG G 472 

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.830 
Fit side-chains
REVERT: B  319 ARG cc_start: 0.7417 (ptp-170) cc_final: 0.7115 (mtm-85)
REVERT: B  358 ASN cc_start: 0.7792 (m-40) cc_final: 0.7252 (m-40)
REVERT: B  420 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7925 (mp10)
REVERT: C  319 ARG cc_start: 0.7907 (mtt180) cc_final: 0.7416 (mtm180)
REVERT: C  322 ARG cc_start: 0.8614 (mtt180) cc_final: 0.8317 (mmm-85)
REVERT: D  396 LYS cc_start: 0.8641 (tttt) cc_final: 0.8413 (tttp)
REVERT: E  305 ILE cc_start: 0.8952 (mm) cc_final: 0.8712 (mt)
REVERT: F  402 GLU cc_start: 0.8347 (mp0) cc_final: 0.8078 (mm-30)
REVERT: F  412 MET cc_start: 0.9016 (mmm) cc_final: 0.8561 (mmt)
REVERT: G  319 ARG cc_start: 0.8441 (mtt-85) cc_final: 0.8098 (mtm180)
  outliers start: 14
  outliers final: 13
  residues processed: 118
  average time/residue: 0.2148
  time to fit residues: 34.2253
Evaluate side-chains
  120 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain C residue  476 ILE
Chi-restraints excluded: chain D residue  316 GLU
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain D residue  369 LEU
Chi-restraints excluded: chain D residue  380 ILE
Chi-restraints excluded: chain D residue  454 GLU
Chi-restraints excluded: chain E residue  423 SER
Chi-restraints excluded: chain F residue  364 THR
Chi-restraints excluded: chain F residue  465 GLU
Chi-restraints excluded: chain F residue  466 ILE
Chi-restraints excluded: chain F residue  475 SER
Chi-restraints excluded: chain G residue  423 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 47 optimal weight:    0.3980
   chunk 12 optimal weight:    0.4980
   chunk 1 optimal weight:    4.9990
   chunk 100 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    0.7382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.100422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.086713 restraints weight = 11085.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.2778 rms_B_bonded: 1.61
r_work: 0.2649 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2516 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.3558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8208  Z= 0.152
  Angle     :  0.470   5.403  11196  Z= 0.235
  Chirality :  0.039   0.137   1314
  Planarity :  0.004   0.032   1470
  Dihedral  :  3.424  11.735   1140
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 1.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 12.99 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.80 (0.27), residues: 1038
  helix:  1.94 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop : -0.88 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 327 
 HIS   0.004   0.001   HIS G 389 
 PHE   0.004   0.001   PHE D 456 
 TYR   0.005   0.001   TYR C 464 
 ARG   0.004   0.000   ARG G 472 

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.819 
Fit side-chains
REVERT: B  319 ARG cc_start: 0.7426 (ptp-170) cc_final: 0.7122 (mtm-85)
REVERT: B  358 ASN cc_start: 0.7714 (m-40) cc_final: 0.7164 (m-40)
REVERT: B  420 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7909 (mp10)
REVERT: C  319 ARG cc_start: 0.7870 (mtt180) cc_final: 0.7429 (mtm180)
REVERT: C  322 ARG cc_start: 0.8656 (mtt180) cc_final: 0.8372 (mmm-85)
REVERT: C  440 GLN cc_start: 0.8526 (tp40) cc_final: 0.8240 (tp-100)
REVERT: D  396 LYS cc_start: 0.8645 (tttt) cc_final: 0.8412 (tttp)
REVERT: E  305 ILE cc_start: 0.8910 (mm) cc_final: 0.8688 (mt)
REVERT: F  402 GLU cc_start: 0.8310 (mp0) cc_final: 0.8100 (mm-30)
REVERT: F  412 MET cc_start: 0.9018 (mmm) cc_final: 0.8555 (mmt)
REVERT: G  319 ARG cc_start: 0.8436 (mtt-85) cc_final: 0.8095 (mtm180)
  outliers start: 15
  outliers final: 13
  residues processed: 120
  average time/residue: 0.2171
  time to fit residues: 34.7550
Evaluate side-chains
  121 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain C residue  476 ILE
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain D residue  369 LEU
Chi-restraints excluded: chain D residue  380 ILE
Chi-restraints excluded: chain D residue  454 GLU
Chi-restraints excluded: chain F residue  336 ASP
Chi-restraints excluded: chain F residue  364 THR
Chi-restraints excluded: chain F residue  465 GLU
Chi-restraints excluded: chain F residue  466 ILE
Chi-restraints excluded: chain F residue  475 SER
Chi-restraints excluded: chain G residue  423 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 14 optimal weight:    7.9990
   chunk 62 optimal weight:    0.0050
   chunk 20 optimal weight:    0.0980
   chunk 71 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 80 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.4996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.102012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.088206 restraints weight = 11190.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.2800 rms_B_bonded: 1.62
r_work: 0.2672 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2538 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.3690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   8208  Z= 0.130
  Angle     :  0.452   5.383  11196  Z= 0.225
  Chirality :  0.038   0.131   1314
  Planarity :  0.004   0.034   1470
  Dihedral  :  3.317  11.917   1140
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 1.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 13.22 %
    Favored  : 85.06 %
  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:  2.00 (0.27), residues: 1038
  helix:  1.99 (0.19), residues: 778
  sheet:  None (None), residues: 0
  loop : -0.71 (0.39), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 327 
 HIS   0.003   0.000   HIS G 389 
 PHE   0.004   0.001   PHE D 456 
 TYR   0.004   0.001   TYR C 464 
 ARG   0.006   0.000   ARG G 472 

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.852 
Fit side-chains
REVERT: B  319 ARG cc_start: 0.7431 (ptp-170) cc_final: 0.7139 (mtm-85)
REVERT: B  420 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7814 (mp10)
REVERT: C  319 ARG cc_start: 0.7814 (mtt180) cc_final: 0.7383 (mtm180)
REVERT: C  322 ARG cc_start: 0.8652 (mtt180) cc_final: 0.8374 (mmm-85)
REVERT: D  396 LYS cc_start: 0.8658 (tttt) cc_final: 0.8437 (tttp)
REVERT: E  305 ILE cc_start: 0.8926 (mm) cc_final: 0.8693 (mt)
REVERT: F  412 MET cc_start: 0.9003 (mmm) cc_final: 0.8505 (mmt)
REVERT: G  319 ARG cc_start: 0.8438 (mtt-85) cc_final: 0.8087 (mtm180)
  outliers start: 15
  outliers final: 13
  residues processed: 110
  average time/residue: 0.2231
  time to fit residues: 32.7997
Evaluate side-chains
  116 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  400 ASP
Chi-restraints excluded: chain C residue  476 ILE
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain D residue  369 LEU
Chi-restraints excluded: chain D residue  380 ILE
Chi-restraints excluded: chain D residue  454 GLU
Chi-restraints excluded: chain F residue  336 ASP
Chi-restraints excluded: chain F residue  364 THR
Chi-restraints excluded: chain F residue  465 GLU
Chi-restraints excluded: chain F residue  466 ILE
Chi-restraints excluded: chain F residue  475 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 57 optimal weight:    6.9990
   chunk 85 optimal weight:    0.7980
   chunk 93 optimal weight:    3.9990
   overall best weight:    1.1182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.099589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.085867 restraints weight = 11362.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.2763 rms_B_bonded: 1.62
r_work: 0.2634 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2501 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.3635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8208  Z= 0.187
  Angle     :  0.477   5.582  11196  Z= 0.237
  Chirality :  0.039   0.136   1314
  Planarity :  0.004   0.032   1470
  Dihedral  :  3.370  12.087   1140
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 1.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 13.22 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.95 (0.27), residues: 1038
  helix:  2.03 (0.19), residues: 756
  sheet:  None (None), residues: 0
  loop : -0.75 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 327 
 HIS   0.004   0.001   HIS G 389 
 PHE   0.005   0.001   PHE F 339 
 TYR   0.006   0.001   TYR C 464 
 ARG   0.006   0.000   ARG G 472 

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.892 
Fit side-chains
REVERT: B  319 ARG cc_start: 0.7397 (ptp-170) cc_final: 0.7113 (mtm180)
REVERT: B  420 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7868 (mp10)
REVERT: C  319 ARG cc_start: 0.7823 (mtt180) cc_final: 0.7382 (mtm180)
REVERT: C  322 ARG cc_start: 0.8671 (mtt180) cc_final: 0.8378 (mmm-85)
REVERT: D  396 LYS cc_start: 0.8666 (tttt) cc_final: 0.8430 (tttp)
REVERT: E  305 ILE cc_start: 0.8930 (mm) cc_final: 0.8683 (mt)
REVERT: F  412 MET cc_start: 0.9041 (mmm) cc_final: 0.8432 (mmt)
REVERT: G  319 ARG cc_start: 0.8457 (mtt-85) cc_final: 0.8112 (mtm180)
  outliers start: 13
  outliers final: 13
  residues processed: 109
  average time/residue: 0.2357
  time to fit residues: 34.2572
Evaluate side-chains
  116 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  400 ASP
Chi-restraints excluded: chain C residue  476 ILE
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain D residue  369 LEU
Chi-restraints excluded: chain D residue  380 ILE
Chi-restraints excluded: chain D residue  454 GLU
Chi-restraints excluded: chain E residue  423 SER
Chi-restraints excluded: chain F residue  336 ASP
Chi-restraints excluded: chain F residue  364 THR
Chi-restraints excluded: chain F residue  465 GLU
Chi-restraints excluded: chain F residue  466 ILE
Chi-restraints excluded: chain F residue  475 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 99 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   overall best weight:    1.8986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.096754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.083187 restraints weight = 11272.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.2723 rms_B_bonded: 1.59
r_work: 0.2594 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2462 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8208  Z= 0.269
  Angle     :  0.529   5.889  11196  Z= 0.265
  Chirality :  0.041   0.154   1314
  Planarity :  0.004   0.032   1470
  Dihedral  :  3.596  14.796   1140
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 2.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 13.45 %
    Favored  : 85.17 %
  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:  1.58 (0.26), residues: 1038
  helix:  1.78 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop : -0.94 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 327 
 HIS   0.006   0.001   HIS G 389 
 PHE   0.008   0.001   PHE F 339 
 TYR   0.008   0.001   TYR C 464 
 ARG   0.006   0.000   ARG G 472 

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.932 
Fit side-chains
REVERT: B  319 ARG cc_start: 0.7470 (ptp-170) cc_final: 0.7215 (mtm180)
REVERT: B  358 ASN cc_start: 0.7948 (m-40) cc_final: 0.7502 (m-40)
REVERT: B  420 GLN cc_start: 0.8330 (mm-40) cc_final: 0.7976 (mp10)
REVERT: C  319 ARG cc_start: 0.7826 (mtt180) cc_final: 0.7329 (mtm180)
REVERT: C  322 ARG cc_start: 0.8714 (mtt180) cc_final: 0.8440 (mmm-85)
REVERT: D  396 LYS cc_start: 0.8675 (tttt) cc_final: 0.8407 (tttp)
REVERT: F  412 MET cc_start: 0.9116 (mmm) cc_final: 0.8604 (mmt)
REVERT: G  319 ARG cc_start: 0.8441 (mtt-85) cc_final: 0.8102 (mtm180)
  outliers start: 12
  outliers final: 12
  residues processed: 110
  average time/residue: 0.2217
  time to fit residues: 32.6841
Evaluate side-chains
  116 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain C residue  476 ILE
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain D residue  369 LEU
Chi-restraints excluded: chain D residue  380 ILE
Chi-restraints excluded: chain D residue  454 GLU
Chi-restraints excluded: chain E residue  423 SER
Chi-restraints excluded: chain F residue  336 ASP
Chi-restraints excluded: chain F residue  364 THR
Chi-restraints excluded: chain F residue  465 GLU
Chi-restraints excluded: chain F residue  466 ILE
Chi-restraints excluded: chain F residue  475 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    1.3186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.098356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.084679 restraints weight = 11253.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.2747 rms_B_bonded: 1.61
r_work: 0.2616 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2483 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.3609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8208  Z= 0.207
  Angle     :  0.496   5.881  11196  Z= 0.247
  Chirality :  0.040   0.141   1314
  Planarity :  0.004   0.032   1470
  Dihedral  :  3.522  14.202   1140
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 1.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 13.33 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.63 (0.26), residues: 1038
  helix:  1.81 (0.19), residues: 756
  sheet:  None (None), residues: 0
  loop : -0.93 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 327 
 HIS   0.005   0.001   HIS G 389 
 PHE   0.006   0.001   PHE F 339 
 TYR   0.006   0.001   TYR C 464 
 ARG   0.006   0.000   ARG G 472 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3781.49 seconds
wall clock time: 65 minutes 23.86 seconds (3923.86 seconds total)