Starting phenix.real_space_refine
on Wed Mar 12 16:02:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ozn_17315/03_2025/8ozn_17315.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ozn_17315/03_2025/8ozn_17315.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ozn_17315/03_2025/8ozn_17315.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ozn_17315/03_2025/8ozn_17315.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ozn_17315/03_2025/8ozn_17315.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ozn_17315/03_2025/8ozn_17315.cif"
  }
  resolution = 3.5
  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    5076      2.51       5
     N    1444      2.21       5
     O    1480      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 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: 8030
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "H"
      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: "I"
      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: "J"
      Number of atoms: 1331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1331
          Classifications: {'peptide': 174}
          Link IDs: {'PTRANS': 11, 'TRANS': 162}
    Chain: "K"
      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: "L"
      Number of atoms: 1331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1331
          Classifications: {'peptide': 174}
          Link IDs: {'PTRANS': 11, 'TRANS': 162}
    Chain: "M"
      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: 6.08, per 1000 atoms: 0.76
  Number of scatterers: 8030
  At special positions: 0
  Unit cell: (115.56, 126.36, 93.96, 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    1480      8.00
     N    1444      7.00
     C    5076      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: 2.00
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1880

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 0 sheets defined
      72.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'H' and resid 306 through 315
      removed outlier: 3.503A  pdb=" N   SER H 312 " --> pdb=" O   GLN H 308 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL H 313 " --> pdb=" O   HIS H 309 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLY H 315 " --> pdb=" O   ARG H 311 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 323 through 339
      Proline residue:  H 333  - end of helix
    Processing helix  chain 'H' and resid 343 through 356
      removed outlier: 3.501A  pdb=" N   ARG H 347 " --> pdb=" O   THR H 343 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 365 through 369
      removed outlier: 3.676A  pdb=" N   LEU H 369 " --> pdb=" O   GLY H 366 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 370 through 384
    Processing helix  chain 'H' and resid 386 through 389
      removed outlier: 3.620A  pdb=" N   HIS H 389 " --> pdb=" O   PHE H 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 386 through 389'
    Processing helix  chain 'H' and resid 390 through 400
      removed outlier: 3.546A  pdb=" N   VAL H 394 " --> pdb=" O   GLN H 390 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LYS H 396 " --> pdb=" O   GLY H 392 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 403 through 414
    Processing helix  chain 'H' and resid 418 through 428
      removed outlier: 3.651A  pdb=" N   VAL H 422 " --> pdb=" O   ASN H 418 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLY H 424 " --> pdb=" O   GLN H 420 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLY H 428 " --> pdb=" O   GLY H 424 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 432 through 443
      removed outlier: 3.705A  pdb=" N   VAL H 436 " --> pdb=" O   GLY H 432 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   THR H 437 " --> pdb=" O   GLN H 433 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 450 through 468
      removed outlier: 6.010A  pdb=" N   ILE H 457 " --> pdb=" O   ALA H 453 " (cutoff:3.500A)
      removed outlier: 5.737A  pdb=" N   GLN H 458 " --> pdb=" O   GLU H 454 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLU H 465 " --> pdb=" O   ASN H 461 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 306 through 314
      removed outlier: 3.724A  pdb=" N   SER I 312 " --> pdb=" O   GLN I 308 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 320 through 322
      No H-bonds generated for 'chain 'I' and resid 320 through 322'
    Processing helix  chain 'I' and resid 323 through 330
    Processing helix  chain 'I' and resid 331 through 339
    Processing helix  chain 'I' and resid 343 through 356
    Processing helix  chain 'I' and resid 370 through 384
    Processing helix  chain 'I' and resid 387 through 389
      No H-bonds generated for 'chain 'I' and resid 387 through 389'
    Processing helix  chain 'I' and resid 390 through 400
    Processing helix  chain 'I' and resid 403 through 414
    Processing helix  chain 'I' and resid 418 through 428
      removed outlier: 3.680A  pdb=" N   VAL I 422 " --> pdb=" O   ASN I 418 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLY I 428 " --> pdb=" O   GLY I 424 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 432 through 445
    Processing helix  chain 'I' and resid 455 through 466
    Processing helix  chain 'J' and resid 306 through 315
      removed outlier: 3.599A  pdb=" N   SER J 312 " --> pdb=" O   GLN J 308 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 323 through 331
      removed outlier: 3.522A  pdb=" N   TRP J 327 " --> pdb=" O   GLU J 323 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 331 through 339
      removed outlier: 3.817A  pdb=" N   ILE J 335 " --> pdb=" O   ASN J 331 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 343 through 355
    Processing helix  chain 'J' and resid 370 through 384
    Processing helix  chain 'J' and resid 387 through 400
      removed outlier: 3.623A  pdb=" N   ASP J 400 " --> pdb=" O   LYS J 396 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 403 through 415
      removed outlier: 3.637A  pdb=" N   ALA J 407 " --> pdb=" O   GLY J 403 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 418 through 427
      removed outlier: 3.596A  pdb=" N   VAL J 422 " --> pdb=" O   ASN J 418 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   GLY J 424 " --> pdb=" O   GLN J 420 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ARG J 427 " --> pdb=" O   SER J 423 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 433 through 446
      removed outlier: 3.731A  pdb=" N   THR J 437 " --> pdb=" O   GLN J 433 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLU J 446 " --> pdb=" O   ARG J 442 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 449 through 455
    Processing helix  chain 'J' and resid 455 through 466
      removed outlier: 3.624A  pdb=" N   ALA J 462 " --> pdb=" O   GLN J 458 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   VAL J 463 " --> pdb=" O   HIS J 459 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 306 through 315
      removed outlier: 3.662A  pdb=" N   ILE K 310 " --> pdb=" O   PRO K 306 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 323 through 331
      removed outlier: 3.511A  pdb=" N   TRP K 327 " --> pdb=" O   GLU K 323 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLY K 329 " --> pdb=" O   PRO K 325 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 331 through 339
    Processing helix  chain 'K' and resid 343 through 356
    Processing helix  chain 'K' and resid 370 through 384
      removed outlier: 3.563A  pdb=" N   LEU K 378 " --> pdb=" O   ALA K 374 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 387 through 400
    Processing helix  chain 'K' and resid 403 through 415
    Processing helix  chain 'K' and resid 418 through 427
      removed outlier: 3.674A  pdb=" N   GLY K 424 " --> pdb=" O   GLN K 420 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 433 through 444
      removed outlier: 3.758A  pdb=" N   THR K 437 " --> pdb=" O   GLN K 433 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ARG K 442 " --> pdb=" O   ALA K 438 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 448 through 455
    Processing helix  chain 'K' and resid 455 through 467
      removed outlier: 3.571A  pdb=" N   VAL K 463 " --> pdb=" O   HIS K 459 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 306 through 314
      removed outlier: 3.793A  pdb=" N   SER L 312 " --> pdb=" O   GLN L 308 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL L 313 " --> pdb=" O   HIS L 309 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 323 through 331
      removed outlier: 3.564A  pdb=" N   ASN L 331 " --> pdb=" O   TRP L 327 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 331 through 339
    Processing helix  chain 'L' and resid 343 through 356
    Processing helix  chain 'L' and resid 370 through 383
      removed outlier: 4.037A  pdb=" N   ALA L 374 " --> pdb=" O   THR L 370 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   VAL L 375 " --> pdb=" O   TRP L 371 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ARG L 381 " --> pdb=" O   THR L 377 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 387 through 389
      No H-bonds generated for 'chain 'L' and resid 387 through 389'
    Processing helix  chain 'L' and resid 390 through 402
    Processing helix  chain 'L' and resid 403 through 414
      removed outlier: 3.639A  pdb=" N   THR L 409 " --> pdb=" O   ALA L 405 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 418 through 427
    Processing helix  chain 'L' and resid 432 through 445
      removed outlier: 3.571A  pdb=" N   THR L 437 " --> pdb=" O   GLN L 433 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 450 through 455
    Processing helix  chain 'L' and resid 455 through 468
      removed outlier: 3.961A  pdb=" N   HIS L 459 " --> pdb=" O   THR L 455 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU L 467 " --> pdb=" O   VAL L 463 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 306 through 315
      removed outlier: 3.766A  pdb=" N   THR M 314 " --> pdb=" O   ILE M 310 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 323 through 330
    Processing helix  chain 'M' and resid 331 through 339
    Processing helix  chain 'M' and resid 343 through 356
      removed outlier: 3.516A  pdb=" N   GLY M 356 " --> pdb=" O   ASN M 352 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 370 through 384
      removed outlier: 3.590A  pdb=" N   ALA M 374 " --> pdb=" O   THR M 370 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 389 through 403
    Processing helix  chain 'M' and resid 403 through 415
      removed outlier: 3.806A  pdb=" N   LEU M 410 " --> pdb=" O   THR M 406 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 418 through 428
      removed outlier: 4.072A  pdb=" N   GLY M 424 " --> pdb=" O   GLN M 420 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLY M 428 " --> pdb=" O   GLY M 424 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 432 through 446
      removed outlier: 3.544A  pdb=" N   THR M 437 " --> pdb=" O   GLN M 433 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ALA M 438 " --> pdb=" O   ALA M 434 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ARG M 442 " --> pdb=" O   ALA M 438 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   GLU M 446 " --> pdb=" O   ARG M 442 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 448 through 455
    Processing helix  chain 'M' and resid 456 through 468

    433 hydrogen bonds defined for protein.
    1296 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: 2.40 seconds

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

  Histogram of bond lengths:
        1.17 -     1.31: 1344
        1.31 -     1.44: 2040
        1.44 -     1.57: 4754
        1.57 -     1.71: 0
        1.71 -     1.84: 48
  Bond restraints: 8186
  Sorted by residual:
  bond pdb=" CA  SER L 415 "
       pdb=" CB  SER L 415 "
    ideal  model  delta    sigma   weight residual
    1.537  1.471  0.066 1.41e-02 5.03e+03 2.20e+01
  bond pdb=" N   MET K 413 "
       pdb=" CA  MET K 413 "
    ideal  model  delta    sigma   weight residual
    1.463  1.513 -0.050 1.08e-02 8.57e+03 2.14e+01
  bond pdb=" C   THR K 406 "
       pdb=" O   THR K 406 "
    ideal  model  delta    sigma   weight residual
    1.236  1.289 -0.053 1.15e-02 7.56e+03 2.11e+01
  bond pdb=" C   VAL M 436 "
       pdb=" O   VAL M 436 "
    ideal  model  delta    sigma   weight residual
    1.236  1.287 -0.050 1.11e-02 8.12e+03 2.06e+01
  bond pdb=" C   CYS L 348 "
       pdb=" O   CYS L 348 "
    ideal  model  delta    sigma   weight residual
    1.236  1.286 -0.049 1.15e-02 7.56e+03 1.85e+01
  ... (remaining 8181 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.94: 9555
        2.94 -     5.88: 1554
        5.88 -     8.82: 56
        8.82 -    11.76: 2
       11.76 -    14.69: 1
  Bond angle restraints: 11168
  Sorted by residual:
  angle pdb=" CA  ARG I 477 "
        pdb=" C   ARG I 477 "
        pdb=" O   ARG I 477 "
      ideal   model   delta    sigma   weight residual
     120.80  135.49  -14.69 1.70e+00 3.46e-01 7.47e+01
  angle pdb=" CA  GLY L 384 "
        pdb=" C   GLY L 384 "
        pdb=" O   GLY L 384 "
      ideal   model   delta    sigma   weight residual
     122.45  117.63    4.82 7.20e-01 1.93e+00 4.49e+01
  angle pdb=" N   PRO J 387 "
        pdb=" CA  PRO J 387 "
        pdb=" CB  PRO J 387 "
      ideal   model   delta    sigma   weight residual
     102.81   98.36    4.45 6.70e-01 2.23e+00 4.41e+01
  angle pdb=" N   PRO J 317 "
        pdb=" CA  PRO J 317 "
        pdb=" CB  PRO J 317 "
      ideal   model   delta    sigma   weight residual
     103.19  106.66   -3.47 5.60e-01 3.19e+00 3.84e+01
  angle pdb=" CA  GLY I 432 "
        pdb=" C   GLY I 432 "
        pdb=" O   GLY I 432 "
      ideal   model   delta    sigma   weight residual
     122.52  117.88    4.64 7.90e-01 1.60e+00 3.46e+01
  ... (remaining 11163 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 4365
       17.65 -    35.30: 391
       35.30 -    52.96: 98
       52.96 -    70.61: 30
       70.61 -    88.26: 8
  Dihedral angle restraints: 4892
    sinusoidal: 1946
      harmonic: 2946
  Sorted by residual:
  dihedral pdb=" CA  LEU H 355 "
           pdb=" C   LEU H 355 "
           pdb=" N   GLY H 356 "
           pdb=" CA  GLY H 356 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.47   29.53     0      5.00e+00 4.00e-02 3.49e+01
  dihedral pdb=" CA  GLY L 403 "
           pdb=" C   GLY L 403 "
           pdb=" N   VAL L 404 "
           pdb=" CA  VAL L 404 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.29   28.71     0      5.00e+00 4.00e-02 3.30e+01
  dihedral pdb=" CA  ASP I 444 "
           pdb=" C   ASP I 444 "
           pdb=" N   GLN I 445 "
           pdb=" CA  GLN I 445 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.76   26.24     0      5.00e+00 4.00e-02 2.75e+01
  ... (remaining 4889 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 620
       0.061 -    0.122: 460
       0.122 -    0.183: 184
       0.183 -    0.243: 43
       0.243 -    0.304: 5
  Chirality restraints: 1312
  Sorted by residual:
  chirality pdb=" CA  PRO K 325 "
            pdb=" N   PRO K 325 "
            pdb=" C   PRO K 325 "
            pdb=" CB  PRO K 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.41    0.30 2.00e-01 2.50e+01 2.31e+00
  chirality pdb=" CA  VAL L 313 "
            pdb=" N   VAL L 313 "
            pdb=" C   VAL L 313 "
            pdb=" CB  VAL L 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.74   -0.30 2.00e-01 2.50e+01 2.30e+00
  chirality pdb=" CA  VAL K 341 "
            pdb=" N   VAL K 341 "
            pdb=" C   VAL K 341 "
            pdb=" CB  VAL K 341 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.70   -0.26 2.00e-01 2.50e+01 1.71e+00
  ... (remaining 1309 not shown)

  Planarity restraints: 1466
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR J 408 "   -0.055 2.00e-02 2.50e+03   3.04e-02 1.85e+01
        pdb=" CG  TYR J 408 "    0.051 2.00e-02 2.50e+03
        pdb=" CD1 TYR J 408 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 TYR J 408 "    0.018 2.00e-02 2.50e+03
        pdb=" CE1 TYR J 408 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR J 408 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR J 408 "   -0.032 2.00e-02 2.50e+03
        pdb=" OH  TYR J 408 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE M 305 "   -0.018 2.00e-02 2.50e+03   3.66e-02 1.34e+01
        pdb=" C   ILE M 305 "    0.063 2.00e-02 2.50e+03
        pdb=" O   ILE M 305 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   PRO M 306 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR K 419 "   -0.046 2.00e-02 2.50e+03   2.36e-02 1.12e+01
        pdb=" CG  TYR K 419 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TYR K 419 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 TYR K 419 "    0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR K 419 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR K 419 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR K 419 "   -0.007 2.00e-02 2.50e+03
        pdb=" OH  TYR K 419 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1463 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 967
        2.78 -     3.31: 8128
        3.31 -     3.84: 11610
        3.84 -     4.37: 15531
        4.37 -     4.90: 24307
  Nonbonded interactions: 60543
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN L 470 "
            pdb=" O   GLN L 474 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   PRO H 321 "
            pdb=" OG1 THR H 382 "
     model   vdw
     2.406 3.040
  nonbonded pdb=" N   GLU I 446 "
            pdb=" O   GLU I 446 "
     model   vdw
     2.430 2.496
  nonbonded pdb=" OD1 ASP L 448 "
            pdb=" N   ASP L 449 "
     model   vdw
     2.456 3.120
  nonbonded pdb=" OG1 THR M 370 "
            pdb=" OD1 ASP M 372 "
     model   vdw
     2.462 3.040
  ... (remaining 60538 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 'H' and resid 303 through 476)
  selection = (chain 'I' and resid 303 through 476)
  selection = chain 'J'
  selection = (chain 'K' and resid 303 through 476)
  selection = chain 'L'
  selection = (chain 'M' and resid 303 through 476)
}

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:             23.040
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.010
  Find NCS groups from input model:        0.410
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7147
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   0.067   8186  Z= 0.967
  Angle     :  2.021  14.694  11168  Z= 1.485
  Chirality :  0.090   0.304   1312
  Planarity :  0.008   0.044   1466
  Dihedral  : 15.491  88.257   3012
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.49 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  8.29 %
    Favored  : 91.59 %
  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: -4.62 (0.19), residues: 1036
  helix: -2.80 (0.14), residues: 704
  sheet:  None (None), residues: 0
  loop : -3.27 (0.27), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.008   TRP K 327 
 HIS   0.015   0.005   HIS I 309 
 PHE   0.039   0.009   PHE L 379 
 TYR   0.055   0.010   TYR J 408 
 ARG   0.014   0.002   ARG I 472 

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 188
  time to evaluate  : 0.903 
Fit side-chains
REVERT: H  420 GLN cc_start: 0.7646 (mt0) cc_final: 0.7360 (mm-40)
REVERT: I  312 SER cc_start: 0.7740 (m) cc_final: 0.7503 (p)
REVERT: J  312 SER cc_start: 0.7804 (t) cc_final: 0.7595 (p)
REVERT: J  388 MET cc_start: 0.5564 (mmp) cc_final: 0.5265 (mmm)
REVERT: J  402 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7873 (mt-10)
REVERT: J  417 GLN cc_start: 0.6179 (mm-40) cc_final: 0.5141 (mm110)
REVERT: J  420 GLN cc_start: 0.8664 (mt0) cc_final: 0.8110 (tm-30)
REVERT: J  427 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6759 (ttp-170)
REVERT: J  452 ARG cc_start: 0.6277 (mtt180) cc_final: 0.5973 (mtt-85)
REVERT: K  359 ILE cc_start: 0.6638 (mt) cc_final: 0.6420 (tp)
REVERT: K  370 THR cc_start: 0.7548 (m) cc_final: 0.7149 (p)
REVERT: K  419 TYR cc_start: 0.7639 (t80) cc_final: 0.7406 (t80)
REVERT: M  319 ARG cc_start: 0.6910 (mtt180) cc_final: 0.6381 (tmm160)
REVERT: M  455 THR cc_start: 0.7550 (m) cc_final: 0.7130 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 188
  average time/residue: 0.3232
  time to fit residues: 73.8254
Evaluate side-chains
  133 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  427 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    7.9990
   chunk 77 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
H 389 HIS
H 458 GLN
I 320 ASN
I 440 GLN
J 352 ASN
J 401 GLN
J 433 GLN
K 433 GLN
L 309 HIS
L 331 ASN
L 474 GLN
M 309 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.107237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.090505 restraints weight = 10981.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.092816 restraints weight = 7619.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.094631 restraints weight = 5826.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8186  Z= 0.245
  Angle     :  0.669   6.744  11168  Z= 0.354
  Chirality :  0.042   0.132   1312
  Planarity :  0.005   0.060   1466
  Dihedral  :  5.160  52.560   1140
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 10.94 %
    Favored  : 87.33 %
  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: -1.86 (0.23), residues: 1036
  helix: -0.61 (0.18), residues: 724
  sheet:  None (None), residues: 0
  loop : -2.54 (0.29), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP K 327 
 HIS   0.006   0.001   HIS H 389 
 PHE   0.012   0.001   PHE J 386 
 TYR   0.013   0.001   TYR M 464 
 ARG   0.005   0.001   ARG K 381 

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.974 
Fit side-chains
REVERT: I  475 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8368 (p)
REVERT: J  348 CYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7596 (p)
REVERT: J  427 ARG cc_start: 0.7358 (mtm110) cc_final: 0.7073 (ttm170)
REVERT: J  452 ARG cc_start: 0.7170 (mtt180) cc_final: 0.6805 (mtt-85)
REVERT: K  370 THR cc_start: 0.8154 (m) cc_final: 0.7898 (p)
REVERT: M  455 THR cc_start: 0.8634 (m) cc_final: 0.8121 (p)
  outliers start: 15
  outliers final: 8
  residues processed: 137
  average time/residue: 0.2512
  time to fit residues: 44.5681
Evaluate side-chains
  119 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  303 THR
Chi-restraints excluded: chain H residue  385 THR
Chi-restraints excluded: chain I residue  475 SER
Chi-restraints excluded: chain J residue  348 CYS
Chi-restraints excluded: chain J residue  475 SER
Chi-restraints excluded: chain K residue  348 CYS
Chi-restraints excluded: chain K residue  426 ILE
Chi-restraints excluded: chain L residue  345 ASP
Chi-restraints excluded: chain L residue  415 SER
Chi-restraints excluded: chain M residue  426 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 74 optimal weight:    0.2980
   chunk 38 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 98 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
H 420 GLN
H 459 HIS
L 352 ASN
L 383 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.108494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.091580 restraints weight = 11156.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.093871 restraints weight = 7761.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.095610 restraints weight = 5958.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8186  Z= 0.184
  Angle     :  0.555   5.710  11168  Z= 0.285
  Chirality :  0.040   0.135   1312
  Planarity :  0.005   0.053   1466
  Dihedral  :  4.163  16.977   1136
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 2.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 13.94 %
    Favored  : 84.79 %
  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: -0.40 (0.25), residues: 1036
  helix:  0.51 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop : -2.04 (0.32), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP K 327 
 HIS   0.003   0.001   HIS M 309 
 PHE   0.009   0.001   PHE J 386 
 TYR   0.006   0.001   TYR L 419 
 ARG   0.004   0.000   ARG J 442 

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
REVERT: J  427 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6757 (ttp-170)
REVERT: L  415 SER cc_start: 0.9124 (OUTLIER) cc_final: 0.8430 (p)
  outliers start: 11
  outliers final: 6
  residues processed: 117
  average time/residue: 0.2519
  time to fit residues: 38.0236
Evaluate side-chains
  103 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  303 THR
Chi-restraints excluded: chain J residue  427 ARG
Chi-restraints excluded: chain K residue  342 THR
Chi-restraints excluded: chain K residue  426 ILE
Chi-restraints excluded: chain L residue  345 ASP
Chi-restraints excluded: chain L residue  415 SER
Chi-restraints excluded: chain M residue  381 ARG
Chi-restraints excluded: chain M residue  426 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0040
   chunk 42 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0020
   chunk 93 optimal weight:    4.9990
   overall best weight:    0.5002

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

Flipped N/Q/H residues before XYZ refinement:
L 352 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.110519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.093642 restraints weight = 11138.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.096064 restraints weight = 7738.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.097842 restraints weight = 5890.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8186  Z= 0.139
  Angle     :  0.507   5.897  11168  Z= 0.257
  Chirality :  0.039   0.130   1312
  Planarity :  0.005   0.059   1466
  Dihedral  :  3.851  15.361   1136
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 14.98 %
    Favored  : 83.64 %
  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:  0.27 (0.26), residues: 1036
  helix:  0.98 (0.20), residues: 726
  sheet:  None (None), residues: 0
  loop : -1.72 (0.32), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP J 327 
 HIS   0.002   0.000   HIS K 309 
 PHE   0.007   0.001   PHE J 386 
 TYR   0.004   0.001   TYR M 464 
 ARG   0.003   0.000   ARG K 381 

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 1.631 
Fit side-chains
   revert: symmetry clash
REVERT: J  427 ARG cc_start: 0.7274 (mtm110) cc_final: 0.6733 (ttp-170)
REVERT: J  441 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7444 (tm-30)
  outliers start: 12
  outliers final: 7
  residues processed: 113
  average time/residue: 0.2566
  time to fit residues: 37.6245
Evaluate side-chains
  100 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  303 THR
Chi-restraints excluded: chain I residue  362 SER
Chi-restraints excluded: chain J residue  342 THR
Chi-restraints excluded: chain K residue  342 THR
Chi-restraints excluded: chain L residue  345 ASP
Chi-restraints excluded: chain M residue  381 ARG
Chi-restraints excluded: chain M residue  426 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0570
   chunk 66 optimal weight:    0.9990
   chunk 83 optimal weight:    6.9990
   chunk 71 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9980
   overall best weight:    0.7702

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

Flipped N/Q/H residues before XYZ refinement:
I 352 ASN
L 352 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.109893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.093267 restraints weight = 11024.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.095545 restraints weight = 7754.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.097212 restraints weight = 5955.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8186  Z= 0.153
  Angle     :  0.502   6.799  11168  Z= 0.253
  Chirality :  0.039   0.140   1312
  Planarity :  0.005   0.059   1466
  Dihedral  :  3.751  14.690   1136
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 14.29 %
    Favored  : 83.53 %
  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:  0.50 (0.26), residues: 1036
  helix:  1.14 (0.20), residues: 727
  sheet:  None (None), residues: 0
  loop : -1.59 (0.33), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP J 327 
 HIS   0.003   0.001   HIS K 459 
 PHE   0.006   0.001   PHE J 386 
 TYR   0.005   0.001   TYR M 464 
 ARG   0.002   0.000   ARG K 381 

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 1.573 
Fit side-chains
   revert: symmetry clash
REVERT: J  427 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6640 (ttp-170)
REVERT: J  441 GLN cc_start: 0.7785 (tm-30) cc_final: 0.7421 (tm-30)
  outliers start: 19
  outliers final: 13
  residues processed: 118
  average time/residue: 0.2909
  time to fit residues: 44.9815
Evaluate side-chains
  111 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  303 THR
Chi-restraints excluded: chain H residue  400 ASP
Chi-restraints excluded: chain I residue  316 GLU
Chi-restraints excluded: chain I residue  362 SER
Chi-restraints excluded: chain J residue  342 THR
Chi-restraints excluded: chain J residue  402 GLU
Chi-restraints excluded: chain J residue  427 ARG
Chi-restraints excluded: chain K residue  326 ILE
Chi-restraints excluded: chain K residue  342 THR
Chi-restraints excluded: chain K residue  426 ILE
Chi-restraints excluded: chain L residue  345 ASP
Chi-restraints excluded: chain M residue  381 ARG
Chi-restraints excluded: chain M residue  382 THR
Chi-restraints excluded: chain M residue  426 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0020
   chunk 0 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 99 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    1.1594

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

Flipped N/Q/H residues before XYZ refinement:
L 352 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.108634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.091960 restraints weight = 11083.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.094233 restraints weight = 7815.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.095823 restraints weight = 6026.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.3494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8186  Z= 0.192
  Angle     :  0.507   5.603  11168  Z= 0.256
  Chirality :  0.039   0.136   1312
  Planarity :  0.005   0.061   1466
  Dihedral  :  3.690  14.755   1136
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 16.47 %
    Favored  : 81.45 %
  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:  0.61 (0.26), residues: 1036
  helix:  1.19 (0.20), residues: 725
  sheet:  None (None), residues: 0
  loop : -1.47 (0.33), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP K 327 
 HIS   0.004   0.001   HIS K 459 
 PHE   0.009   0.001   PHE K 456 
 TYR   0.009   0.001   TYR M 464 
 ARG   0.002   0.000   ARG J 311 

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
REVERT: I  369 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8227 (mp)
REVERT: J  427 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6806 (ttp80)
REVERT: J  441 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7445 (tm-30)
REVERT: L  415 SER cc_start: 0.9212 (OUTLIER) cc_final: 0.8487 (p)
  outliers start: 18
  outliers final: 11
  residues processed: 108
  average time/residue: 0.2882
  time to fit residues: 39.7835
Evaluate side-chains
  106 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  303 THR
Chi-restraints excluded: chain I residue  362 SER
Chi-restraints excluded: chain I residue  369 LEU
Chi-restraints excluded: chain I residue  380 ILE
Chi-restraints excluded: chain J residue  342 THR
Chi-restraints excluded: chain J residue  399 VAL
Chi-restraints excluded: chain J residue  402 GLU
Chi-restraints excluded: chain J residue  427 ARG
Chi-restraints excluded: chain K residue  426 ILE
Chi-restraints excluded: chain L residue  303 THR
Chi-restraints excluded: chain L residue  345 ASP
Chi-restraints excluded: chain L residue  415 SER
Chi-restraints excluded: chain M residue  381 ARG
Chi-restraints excluded: chain M residue  426 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 89 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 96 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0370
   chunk 32 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0070
   chunk 26 optimal weight:    4.9990
   overall best weight:    1.6082

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

Flipped N/Q/H residues before XYZ refinement:
L 352 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.107114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.090471 restraints weight = 11234.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.092696 restraints weight = 7905.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.094368 restraints weight = 6104.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.3551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8186  Z= 0.233
  Angle     :  0.525   5.938  11168  Z= 0.265
  Chirality :  0.040   0.141   1312
  Planarity :  0.005   0.061   1466
  Dihedral  :  3.753  14.900   1136
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.36 %
    Favored  : 81.22 %
  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:  0.53 (0.26), residues: 1036
  helix:  1.12 (0.19), residues: 727
  sheet:  None (None), residues: 0
  loop : -1.45 (0.33), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP K 327 
 HIS   0.005   0.001   HIS K 459 
 PHE   0.010   0.001   PHE K 456 
 TYR   0.010   0.001   TYR M 464 
 ARG   0.003   0.000   ARG K 349 

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
REVERT: I  369 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8261 (mp)
REVERT: J  427 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6709 (ttp-170)
REVERT: J  441 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7455 (tm-30)
REVERT: K  419 TYR cc_start: 0.8777 (t80) cc_final: 0.8466 (t80)
REVERT: L  308 GLN cc_start: 0.7846 (pm20) cc_final: 0.7597 (pm20)
REVERT: L  319 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7618 (mtp85)
REVERT: L  415 SER cc_start: 0.9238 (OUTLIER) cc_final: 0.8476 (p)
REVERT: L  472 ARG cc_start: 0.8294 (mtp-110) cc_final: 0.7987 (mtt90)
  outliers start: 21
  outliers final: 17
  residues processed: 112
  average time/residue: 0.2677
  time to fit residues: 38.3052
Evaluate side-chains
  115 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  303 THR
Chi-restraints excluded: chain H residue  307 ILE
Chi-restraints excluded: chain H residue  400 ASP
Chi-restraints excluded: chain I residue  362 SER
Chi-restraints excluded: chain I residue  369 LEU
Chi-restraints excluded: chain I residue  380 ILE
Chi-restraints excluded: chain J residue  342 THR
Chi-restraints excluded: chain J residue  343 THR
Chi-restraints excluded: chain J residue  399 VAL
Chi-restraints excluded: chain J residue  402 GLU
Chi-restraints excluded: chain J residue  427 ARG
Chi-restraints excluded: chain K residue  426 ILE
Chi-restraints excluded: chain K residue  458 GLN
Chi-restraints excluded: chain L residue  303 THR
Chi-restraints excluded: chain L residue  345 ASP
Chi-restraints excluded: chain L residue  415 SER
Chi-restraints excluded: chain L residue  426 ILE
Chi-restraints excluded: chain M residue  381 ARG
Chi-restraints excluded: chain M residue  413 MET
Chi-restraints excluded: chain M residue  426 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0470
   chunk 60 optimal weight:    0.9990
   chunk 29 optimal weight:    0.3980
   chunk 93 optimal weight:    0.6980
   chunk 71 optimal weight:    0.0870
   chunk 81 optimal weight:    1.9990
   chunk 76 optimal weight:    0.1980
   chunk 69 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   overall best weight:    0.2856

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

Flipped N/Q/H residues before XYZ refinement:
L 352 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.111598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.095003 restraints weight = 11206.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.097244 restraints weight = 7806.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.099008 restraints weight = 5990.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.3819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8186  Z= 0.125
  Angle     :  0.475   6.331  11168  Z= 0.237
  Chirality :  0.038   0.129   1312
  Planarity :  0.004   0.060   1466
  Dihedral  :  3.537  14.235   1136
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 17.63 %
    Favored  : 80.76 %
  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:  1.01 (0.27), residues: 1036
  helix:  1.47 (0.20), residues: 730
  sheet:  None (None), residues: 0
  loop : -1.30 (0.33), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP J 327 
 HIS   0.004   0.001   HIS K 459 
 PHE   0.005   0.001   PHE L 386 
 TYR   0.005   0.001   TYR I 464 
 ARG   0.001   0.000   ARG M 311 

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.846 
Fit side-chains
REVERT: J  412 MET cc_start: 0.7936 (mmm) cc_final: 0.7670 (mmm)
REVERT: J  427 ARG cc_start: 0.7142 (mtm110) cc_final: 0.6659 (ttp-170)
REVERT: J  441 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7411 (tm-30)
REVERT: L  319 ARG cc_start: 0.7825 (mtp180) cc_final: 0.7602 (mtp85)
REVERT: M  381 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7502 (ttm170)
  outliers start: 14
  outliers final: 9
  residues processed: 116
  average time/residue: 0.2592
  time to fit residues: 38.4147
Evaluate side-chains
  107 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  303 THR
Chi-restraints excluded: chain I residue  362 SER
Chi-restraints excluded: chain J residue  342 THR
Chi-restraints excluded: chain J residue  402 GLU
Chi-restraints excluded: chain K residue  326 ILE
Chi-restraints excluded: chain K residue  426 ILE
Chi-restraints excluded: chain L residue  303 THR
Chi-restraints excluded: chain L residue  345 ASP
Chi-restraints excluded: chain M residue  381 ARG
Chi-restraints excluded: chain M residue  413 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 46 optimal weight:    0.4980
   chunk 43 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0770
   chunk 59 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0370
   overall best weight:    0.7218

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

Flipped N/Q/H residues before XYZ refinement:
L 352 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.110517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.093783 restraints weight = 11351.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.096044 restraints weight = 7968.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.097751 restraints weight = 6107.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.3852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8186  Z= 0.148
  Angle     :  0.490   8.164  11168  Z= 0.242
  Chirality :  0.038   0.130   1312
  Planarity :  0.005   0.061   1466
  Dihedral  :  3.496  14.447   1136
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 18.32 %
    Favored  : 80.41 %
  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 (0.27), residues: 1036
  helix:  1.51 (0.20), residues: 735
  sheet:  None (None), residues: 0
  loop : -1.23 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP J 327 
 HIS   0.006   0.001   HIS K 459 
 PHE   0.006   0.001   PHE L 456 
 TYR   0.004   0.001   TYR M 464 
 ARG   0.002   0.000   ARG K 472 

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.929 
Fit side-chains
REVERT: I  369 LEU cc_start: 0.8425 (tp) cc_final: 0.8188 (mp)
REVERT: J  412 MET cc_start: 0.7941 (mmm) cc_final: 0.7704 (mmm)
REVERT: J  427 ARG cc_start: 0.7177 (mtm110) cc_final: 0.6685 (ttp-170)
REVERT: J  441 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7393 (tm-30)
REVERT: K  419 TYR cc_start: 0.8799 (t80) cc_final: 0.8505 (t80)
REVERT: L  319 ARG cc_start: 0.7866 (mtp180) cc_final: 0.7646 (mtp85)
REVERT: L  472 ARG cc_start: 0.8233 (mtp-110) cc_final: 0.7954 (mtt90)
REVERT: M  381 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7512 (ttm170)
  outliers start: 11
  outliers final: 10
  residues processed: 109
  average time/residue: 0.2547
  time to fit residues: 35.8338
Evaluate side-chains
  110 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  303 THR
Chi-restraints excluded: chain I residue  362 SER
Chi-restraints excluded: chain J residue  342 THR
Chi-restraints excluded: chain J residue  399 VAL
Chi-restraints excluded: chain J residue  402 GLU
Chi-restraints excluded: chain K residue  326 ILE
Chi-restraints excluded: chain K residue  426 ILE
Chi-restraints excluded: chain L residue  303 THR
Chi-restraints excluded: chain M residue  381 ARG
Chi-restraints excluded: chain M residue  413 MET
Chi-restraints excluded: chain M residue  426 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 67 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 92 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
L 352 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.110369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.094813 restraints weight = 11204.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.096764 restraints weight = 8270.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.098228 restraints weight = 6554.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.3881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8186  Z= 0.158
  Angle     :  0.493   8.470  11168  Z= 0.242
  Chirality :  0.039   0.131   1312
  Planarity :  0.004   0.061   1466
  Dihedral  :  3.480  14.525   1136
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 1.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 18.55 %
    Favored  : 80.07 %
  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:  1.08 (0.27), residues: 1036
  helix:  1.47 (0.20), residues: 738
  sheet:  None (None), residues: 0
  loop : -1.18 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K 327 
 HIS   0.006   0.001   HIS K 459 
 PHE   0.007   0.001   PHE K 456 
 TYR   0.005   0.001   TYR M 464 
 ARG   0.002   0.000   ARG K 330 

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.957 
Fit side-chains
REVERT: I  369 LEU cc_start: 0.8401 (tp) cc_final: 0.8173 (mp)
REVERT: J  342 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7794 (p)
REVERT: J  412 MET cc_start: 0.7948 (mmm) cc_final: 0.7722 (mmm)
REVERT: J  427 ARG cc_start: 0.7161 (mtm110) cc_final: 0.6656 (ttp-170)
REVERT: J  441 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7460 (tm-30)
REVERT: K  419 TYR cc_start: 0.8802 (t80) cc_final: 0.8469 (t80)
REVERT: L  319 ARG cc_start: 0.7858 (mtp180) cc_final: 0.7649 (mtp85)
REVERT: L  472 ARG cc_start: 0.8247 (mtp-110) cc_final: 0.7952 (mtt90)
REVERT: M  381 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7594 (ttm170)
  outliers start: 12
  outliers final: 10
  residues processed: 119
  average time/residue: 0.2639
  time to fit residues: 40.3673
Evaluate side-chains
  115 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  303 THR
Chi-restraints excluded: chain H residue  400 ASP
Chi-restraints excluded: chain I residue  362 SER
Chi-restraints excluded: chain J residue  342 THR
Chi-restraints excluded: chain J residue  399 VAL
Chi-restraints excluded: chain J residue  402 GLU
Chi-restraints excluded: chain K residue  326 ILE
Chi-restraints excluded: chain K residue  426 ILE
Chi-restraints excluded: chain L residue  303 THR
Chi-restraints excluded: chain M residue  381 ARG
Chi-restraints excluded: chain M residue  413 MET
Chi-restraints excluded: chain M residue  426 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 89 optimal weight:    7.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
L 352 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.108505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.091758 restraints weight = 11308.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.094011 restraints weight = 7873.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.095741 restraints weight = 6022.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.3925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8186  Z= 0.163
  Angle     :  0.496   8.547  11168  Z= 0.243
  Chirality :  0.039   0.131   1312
  Planarity :  0.004   0.061   1466
  Dihedral  :  3.477  14.639   1136
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 1.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 18.66 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.27), residues: 1036
  helix:  1.48 (0.20), residues: 738
  sheet:  None (None), residues: 0
  loop : -1.15 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K 327 
 HIS   0.005   0.001   HIS K 459 
 PHE   0.007   0.001   PHE K 456 
 TYR   0.005   0.001   TYR M 464 
 ARG   0.002   0.000   ARG K 472 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2906.54 seconds
wall clock time: 52 minutes 3.24 seconds (3123.24 seconds total)