Starting phenix.real_space_refine
on Thu Mar  6 05:07:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ke9_37150/03_2025/8ke9_37150_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ke9_37150/03_2025/8ke9_37150.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ke9_37150/03_2025/8ke9_37150.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ke9_37150/03_2025/8ke9_37150.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ke9_37150/03_2025/8ke9_37150_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ke9_37150/03_2025/8ke9_37150_neut.cif"
  }
  resolution = 3.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    3105      2.51       5
     N     837      2.21       5
     O     987      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 4929
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1643
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 211}
    Chain: "B"
      Number of atoms: 1643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1643
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 211}
    Chain: "C"
      Number of atoms: 1643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1643
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 211}
  Time building chain proxies: 3.86, per 1000 atoms: 0.78
  Number of scatterers: 4929
  At special positions: 0
  Unit cell: (66.34, 142.31, 100.58, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     987      8.00
     N     837      7.00
     C    3105      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: 1.31
  Conformation dependent library (CDL) restraints added in 648.4 milliseconds
  

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1170

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 11 sheets defined
      20.3% alpha, 36.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 245 through 266
      removed outlier: 3.789A  pdb=" N   VAL A 249 " --> pdb=" O   ASP A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 280
    Processing helix  chain 'A' and resid 307 through 318
    Processing helix  chain 'B' and resid 247 through 266
    Processing helix  chain 'B' and resid 269 through 279
    Processing helix  chain 'B' and resid 307 through 317
    Processing helix  chain 'C' and resid 246 through 267
    Processing helix  chain 'C' and resid 269 through 280
    Processing helix  chain 'C' and resid 307 through 317
    Processing sheet with id=AA1, first strand: chain 'A' and resid 328 through 330
      removed outlier: 4.096A  pdb=" N   VAL A 454 " --> pdb=" O   THR A 374 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   THR A 374 " --> pdb=" O   VAL A 454 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   PHE A 456 " --> pdb=" O   THR A 372 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   THR A 372 " --> pdb=" O   PHE A 456 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   GLY A 458 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   LEU A 370 " --> pdb=" O   GLY A 458 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 345 through 348
      removed outlier: 3.525A  pdb=" N   PHE A 321 " --> pdb=" O   GLY A 458 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   GLY A 458 " --> pdb=" O   PHE A 321 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   VAL A 454 " --> pdb=" O   THR A 374 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   THR A 374 " --> pdb=" O   VAL A 454 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   PHE A 456 " --> pdb=" O   THR A 372 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   THR A 372 " --> pdb=" O   PHE A 456 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   GLY A 458 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   LEU A 370 " --> pdb=" O   GLY A 458 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLY A 423 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 340
      removed outlier: 6.717A  pdb=" N   VAL A 394 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   PHE A 404 " --> pdb=" O   VAL A 394 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 355 through 357
    Processing sheet with id=AA5, first strand: chain 'B' and resid 328 through 330
      removed outlier: 3.521A  pdb=" N   GLY B 458 " --> pdb=" O   PHE B 321 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   PHE B 321 " --> pdb=" O   GLY B 458 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 328 through 330
      removed outlier: 4.861A  pdb=" N   VAL B 449 " --> pdb=" O   VAL B 380 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   VAL B 380 " --> pdb=" O   VAL B 449 " (cutoff:3.500A)
      removed outlier: 5.347A  pdb=" N   LEU B 451 " --> pdb=" O   ALA B 378 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   ALA B 378 " --> pdb=" O   LEU B 451 " (cutoff:3.500A)
      removed outlier: 5.415A  pdb=" N   ASP B 453 " --> pdb=" O   ARG B 376 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   ARG B 376 " --> pdb=" O   ASP B 453 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 339 through 340
      removed outlier: 3.579A  pdb=" N   ASN B 436 " --> pdb=" O   PHE B 393 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   ALA B 390 " --> pdb=" O   ARG B 407 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   ARG B 407 " --> pdb=" O   ALA B 390 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   LEU B 392 " --> pdb=" O   LEU B 405 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 355 through 357
      removed outlier: 3.627A  pdb=" N   ASN B 355 " --> pdb=" O   LEU B 362 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 345 through 348
      removed outlier: 4.177A  pdb=" N   PHE C 321 " --> pdb=" O   GLY C 458 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   VAL C 454 " --> pdb=" O   ARG C 325 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   GLY C 327 " --> pdb=" O   GLU C 452 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   GLU C 452 " --> pdb=" O   GLY C 327 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   GLN C 329 " --> pdb=" O   VAL C 450 " (cutoff:3.500A)
      removed outlier: 5.094A  pdb=" N   VAL C 450 " --> pdb=" O   GLN C 329 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   SER C 448 " --> pdb=" O   VAL C 380 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   VAL C 380 " --> pdb=" O   SER C 448 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   VAL C 454 " --> pdb=" O   THR C 374 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   THR C 374 " --> pdb=" O   VAL C 454 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   PHE C 456 " --> pdb=" O   THR C 372 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   THR C 372 " --> pdb=" O   PHE C 456 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   GLY C 458 " --> pdb=" O   LEU C 370 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   LEU C 370 " --> pdb=" O   GLY C 458 " (cutoff:3.500A)
      removed outlier: 5.085A  pdb=" N   GLN C 460 " --> pdb=" O   THR C 368 " (cutoff:3.500A)
      removed outlier: 7.429A  pdb=" N   THR C 368 " --> pdb=" O   GLN C 460 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 339 through 340
      removed outlier: 3.755A  pdb=" N   ASN C 436 " --> pdb=" O   PHE C 393 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   PHE C 393 " --> pdb=" O   ASN C 436 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLN C 438 " --> pdb=" O   LEU C 391 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   ALA C 390 " --> pdb=" O   ARG C 407 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   ARG C 407 " --> pdb=" O   ALA C 390 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   LEU C 392 " --> pdb=" O   LEU C 405 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 355 through 356
      removed outlier: 3.604A  pdb=" N   ASN C 355 " --> pdb=" O   LEU C 362 " (cutoff:3.500A)

    227 hydrogen bonds defined for protein.
    609 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: 1.43

  Time building geometry restraints manager: 1.55 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 813
        1.29 -     1.35: 825
        1.35 -     1.42: 597
        1.42 -     1.49: 799
        1.49 -     1.56: 2000
  Bond restraints: 5034
  Sorted by residual:
  bond pdb=" C   VAL B 273 "
       pdb=" O   VAL B 273 "
    ideal  model  delta    sigma   weight residual
    1.237  1.219  0.018 1.19e-02 7.06e+03 2.27e+00
  bond pdb=" CA  VAL B 273 "
       pdb=" CB  VAL B 273 "
    ideal  model  delta    sigma   weight residual
    1.540  1.557 -0.018 1.29e-02 6.01e+03 1.90e+00
  bond pdb=" C   TYR C 248 "
       pdb=" O   TYR C 248 "
    ideal  model  delta    sigma   weight residual
    1.236  1.221  0.015 1.15e-02 7.56e+03 1.77e+00
  bond pdb=" C   LEU A 270 "
       pdb=" O   LEU A 270 "
    ideal  model  delta    sigma   weight residual
    1.236  1.220  0.016 1.21e-02 6.83e+03 1.71e+00
  bond pdb=" C   VAL A 249 "
       pdb=" O   VAL A 249 "
    ideal  model  delta    sigma   weight residual
    1.237  1.222  0.015 1.17e-02 7.31e+03 1.61e+00
  ... (remaining 5029 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.63: 6801
        2.63 -     5.26: 65
        5.26 -     7.89: 7
        7.89 -    10.52: 3
       10.52 -    13.15: 3
  Bond angle restraints: 6879
  Sorted by residual:
  angle pdb=" C   VAL A 287 "
        pdb=" N   LEU A 288 "
        pdb=" CA  LEU A 288 "
      ideal   model   delta    sigma   weight residual
     122.93  136.08  -13.15 1.45e+00 4.76e-01 8.23e+01
  angle pdb=" C   ASN A 282 "
        pdb=" N   LEU A 283 "
        pdb=" CA  LEU A 283 "
      ideal   model   delta    sigma   weight residual
     120.28  131.22  -10.94 1.34e+00 5.57e-01 6.67e+01
  angle pdb=" N   LEU B 253 "
        pdb=" CA  LEU B 253 "
        pdb=" C   LEU B 253 "
      ideal   model   delta    sigma   weight residual
     111.07  105.54    5.53 1.07e+00 8.73e-01 2.67e+01
  angle pdb=" N   LEU A 270 "
        pdb=" CA  LEU A 270 "
        pdb=" C   LEU A 270 "
      ideal   model   delta    sigma   weight residual
     111.37  119.28   -7.91 1.64e+00 3.72e-01 2.33e+01
  angle pdb=" N   LYS B 267 "
        pdb=" CA  LYS B 267 "
        pdb=" C   LYS B 267 "
      ideal   model   delta    sigma   weight residual
     108.45  113.49   -5.04 1.26e+00 6.30e-01 1.60e+01
  ... (remaining 6874 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 2649
       17.77 -    35.55: 143
       35.55 -    53.32: 47
       53.32 -    71.09: 18
       71.09 -    88.87: 8
  Dihedral angle restraints: 2865
    sinusoidal: 1017
      harmonic: 1848
  Sorted by residual:
  dihedral pdb=" CA  ASN B 284 "
           pdb=" C   ASN B 284 "
           pdb=" N   GLY B 285 "
           pdb=" CA  GLY B 285 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.22  -19.78     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" C   ASN B 290 "
           pdb=" N   ASN B 290 "
           pdb=" CA  ASN B 290 "
           pdb=" CB  ASN B 290 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.12    9.52     0      2.50e+00 1.60e-01 1.45e+01
  dihedral pdb=" C   VAL B 273 "
           pdb=" N   VAL B 273 "
           pdb=" CA  VAL B 273 "
           pdb=" CB  VAL B 273 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.19    9.19     0      2.50e+00 1.60e-01 1.35e+01
  ... (remaining 2862 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.345: 793
       0.345 -    0.689: 4
       0.689 -    1.034: 0
       1.034 -    1.379: 0
       1.379 -    1.723: 1
  Chirality restraints: 798
  Sorted by residual:
  chirality pdb=" CG  LEU B 283 "
            pdb=" CB  LEU B 283 "
            pdb=" CD1 LEU B 283 "
            pdb=" CD2 LEU B 283 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.87   -1.72 2.00e-01 2.50e+01 7.42e+01
  chirality pdb=" CA  LEU B 288 "
            pdb=" N   LEU B 288 "
            pdb=" C   LEU B 288 "
            pdb=" CB  LEU B 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.08e+00
  chirality pdb=" CA  LEU A 288 "
            pdb=" N   LEU A 288 "
            pdb=" C   LEU A 288 "
            pdb=" CB  LEU A 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.22e+00
  ... (remaining 795 not shown)

  Planarity restraints: 897
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 273 "   -0.005 2.00e-02 2.50e+03   1.11e-02 1.22e+00
        pdb=" C   VAL B 273 "    0.019 2.00e-02 2.50e+03
        pdb=" O   VAL B 273 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   ASN B 274 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 412 "   -0.016 5.00e-02 4.00e+02   2.49e-02 9.94e-01
        pdb=" N   PRO A 413 "    0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO A 413 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 413 "   -0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 249 "   -0.005 2.00e-02 2.50e+03   9.15e-03 8.37e-01
        pdb=" C   VAL A 249 "    0.016 2.00e-02 2.50e+03
        pdb=" O   VAL A 249 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   ASN A 250 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 894 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 87
        2.52 -     3.12: 4191
        3.12 -     3.71: 8315
        3.71 -     4.31: 11712
        4.31 -     4.90: 19104
  Nonbonded interactions: 43409
  Sorted by model distance:
  nonbonded pdb=" O   GLN C 276 "
            pdb=" OG  SER C 279 "
     model   vdw
     1.931 3.040
  nonbonded pdb=" O   GLU B 365 "
            pdb=" OH  TYR B 369 "
     model   vdw
     2.001 3.040
  nonbonded pdb=" OG1 THR A 340 "
            pdb=" OD1 ASN A 436 "
     model   vdw
     2.019 3.040
  nonbonded pdb=" OG  SER A 333 "
            pdb=" OG  SER A 335 "
     model   vdw
     2.039 3.040
  nonbonded pdb=" OG1 THR B 303 "
            pdb=" OG1 THR C 292 "
     model   vdw
     2.050 3.040
  ... (remaining 43404 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     17.100
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5034  Z= 0.203
  Angle     :  0.704  13.153   6879  Z= 0.417
  Chirality :  0.081   1.723    798
  Planarity :  0.003   0.030    897
  Dihedral  : 14.469  88.867   1695
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.71 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  7.55 %
    Allowed  :  6.81 %
    Favored  : 85.64 %
  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: -1.09 (0.32), residues: 648
  helix: -0.53 (0.41), residues: 132
  sheet:  0.26 (0.36), residues: 222
  loop : -1.58 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 361 
 HIS   0.002   0.001   HIS C 310 
 PHE   0.015   0.001   PHE B 321 
 TYR   0.007   0.001   TYR A 387 
 ARG   0.005   0.001   ARG B 376 

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 91
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.9393 (m) cc_final: 0.9031 (p)
REVERT: A  344 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7116 (m-40)
REVERT: A  365 GLU cc_start: 0.8762 (tt0) cc_final: 0.8146 (tt0)
REVERT: B  391 LEU cc_start: 0.8550 (mp) cc_final: 0.8014 (tt)
REVERT: B  419 LEU cc_start: 0.7695 (mp) cc_final: 0.7341 (tt)
REVERT: C  365 GLU cc_start: 0.8504 (tt0) cc_final: 0.8298 (mm-30)
REVERT: C  371 ILE cc_start: 0.8179 (mm) cc_final: 0.7833 (mp)
REVERT: C  425 LEU cc_start: 0.8647 (mt) cc_final: 0.8371 (mt)
  outliers start: 41
  outliers final: 7
  residues processed: 115
  average time/residue: 0.1967
  time to fit residues: 28.1030
Evaluate side-chains
  62 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  344 ASN
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  261 ASP
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  282 ASN
Chi-restraints excluded: chain C residue  260 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 47 optimal weight:   20.0000
   chunk 26 optimal weight:   20.0000
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 25 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 19 optimal weight:   30.0000
   chunk 30 optimal weight:   20.0000
   chunk 36 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
B 440 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.047435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.038524 restraints weight = 38798.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.039700 restraints weight = 25258.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.040584 restraints weight = 18333.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5034  Z= 0.275
  Angle     :  0.690   9.387   6879  Z= 0.360
  Chirality :  0.046   0.212    798
  Planarity :  0.004   0.030    897
  Dihedral  :  6.927  57.340    724
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 12.71 %
    Favored  : 83.61 %
  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: -0.59 (0.33), residues: 648
  helix:  0.45 (0.43), residues: 135
  sheet:  0.23 (0.35), residues: 231
  loop : -1.31 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 361 
 HIS   0.004   0.001   HIS B 310 
 PHE   0.021   0.002   PHE A 434 
 TYR   0.023   0.002   TYR A 248 
 ARG   0.006   0.001   ARG C 376 

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 GLU cc_start: 0.8661 (tt0) cc_final: 0.8134 (tt0)
REVERT: A  389 ASP cc_start: 0.7451 (t0) cc_final: 0.6589 (t0)
REVERT: C  412 TYR cc_start: 0.8944 (m-80) cc_final: 0.8540 (m-80)
  outliers start: 20
  outliers final: 13
  residues processed: 64
  average time/residue: 0.1633
  time to fit residues: 13.7588
Evaluate side-chains
  55 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  261 ASP
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  282 ASN
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  393 PHE
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain C residue  267 LYS
Chi-restraints excluded: chain C residue  269 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 54 optimal weight:    7.9990
   chunk 21 optimal weight:    6.9990
   chunk 3 optimal weight:   20.0000
   chunk 31 optimal weight:    0.0050
   chunk 40 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 4 optimal weight:    9.9990
   chunk 5 optimal weight:    0.0370
   chunk 47 optimal weight:   20.0000
   chunk 33 optimal weight:    5.9990
   chunk 18 optimal weight:   20.0000
   overall best weight:    4.2078

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.046679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.038434 restraints weight = 41460.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.039575 restraints weight = 26614.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.040371 restraints weight = 19140.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.4056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5034  Z= 0.220
  Angle     :  0.649  10.111   6879  Z= 0.331
  Chirality :  0.045   0.212    798
  Planarity :  0.004   0.080    897
  Dihedral  :  6.027  46.268    715
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.71 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 12.89 %
    Favored  : 83.24 %
  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: -0.20 (0.33), residues: 648
  helix:  1.24 (0.43), residues: 135
  sheet:  0.30 (0.36), residues: 227
  loop : -1.15 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 361 
 HIS   0.003   0.001   HIS C 310 
 PHE   0.017   0.002   PHE A 393 
 TYR   0.012   0.002   TYR A 417 
 ARG   0.007   0.001   ARG C 376 

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 46
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.9592 (m) cc_final: 0.9357 (p)
REVERT: A  365 GLU cc_start: 0.8675 (tt0) cc_final: 0.8182 (tt0)
REVERT: A  369 TYR cc_start: 0.8291 (m-80) cc_final: 0.7866 (m-80)
REVERT: B  263 LEU cc_start: 0.9391 (mt) cc_final: 0.9124 (pp)
REVERT: B  365 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8303 (tm-30)
REVERT: C  365 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7027 (mm-30)
REVERT: C  371 ILE cc_start: 0.7477 (mm) cc_final: 0.6895 (mp)
REVERT: C  412 TYR cc_start: 0.8900 (m-80) cc_final: 0.8547 (m-80)
  outliers start: 21
  outliers final: 15
  residues processed: 59
  average time/residue: 0.1306
  time to fit residues: 11.1718
Evaluate side-chains
  57 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 42
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  393 PHE
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  282 ASN
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain C residue  267 LYS
Chi-restraints excluded: chain C residue  269 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 47 optimal weight:    8.9990
   chunk 11 optimal weight:    2.9990
   chunk 12 optimal weight:    7.9990
   chunk 13 optimal weight:   30.0000
   chunk 57 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 51 optimal weight:    8.9990
   chunk 6 optimal weight:   10.0000
   chunk 55 optimal weight:   40.0000
   chunk 59 optimal weight:   20.0000
   chunk 1 optimal weight:   10.0000
   overall best weight:    7.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 310 HIS
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 310 HIS
C 409 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.041524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.033195 restraints weight = 40655.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.034307 restraints weight = 25353.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.035105 restraints weight = 17998.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.5275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   5034  Z= 0.336
  Angle     :  0.685   8.419   6879  Z= 0.353
  Chirality :  0.044   0.191    798
  Planarity :  0.005   0.072    897
  Dihedral  :  6.172  48.631    713
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 18.32
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.94 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 12.15 %
    Favored  : 82.50 %
  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: -0.57 (0.33), residues: 648
  helix:  0.87 (0.44), residues: 135
  sheet:  0.11 (0.36), residues: 223
  loop : -1.36 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 352 
 HIS   0.004   0.001   HIS C 310 
 PHE   0.020   0.002   PHE B 434 
 TYR   0.022   0.002   TYR A 417 
 ARG   0.006   0.001   ARG C 376 

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 35
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  267 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8562 (mmtt)
REVERT: B  365 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8400 (tm-30)
REVERT: C  267 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8578 (mmmt)
REVERT: C  412 TYR cc_start: 0.9057 (m-80) cc_final: 0.8764 (m-80)
  outliers start: 29
  outliers final: 17
  residues processed: 55
  average time/residue: 0.1517
  time to fit residues: 12.0497
Evaluate side-chains
  49 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 30
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  393 PHE
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  434 PHE
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  282 ASN
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  344 ASN
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain C residue  267 LYS
Chi-restraints excluded: chain C residue  269 ASP
Chi-restraints excluded: chain C residue  409 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 32 optimal weight:    0.5980
   chunk 52 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 33 optimal weight:    9.9990
   chunk 39 optimal weight:    9.9990
   chunk 8 optimal weight:    8.9990
   chunk 53 optimal weight:    1.9990
   chunk 3 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    3.9188

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

Flipped N/Q/H residues before XYZ refinement:
B 403 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.042203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.033851 restraints weight = 39321.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.035025 restraints weight = 23927.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.035871 restraints weight = 16686.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.5655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5034  Z= 0.212
  Angle     :  0.635  13.026   6879  Z= 0.318
  Chirality :  0.043   0.150    798
  Planarity :  0.004   0.064    897
  Dihedral  :  5.944  49.449    713
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 15.01
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.86 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 16.02 %
    Favored  : 80.85 %
  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: -0.44 (0.33), residues: 648
  helix:  1.18 (0.45), residues: 135
  sheet:  0.23 (0.37), residues: 210
  loop : -1.36 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 361 
 HIS   0.003   0.001   HIS A 310 
 PHE   0.021   0.002   PHE A 434 
 TYR   0.026   0.002   TYR A 387 
 ARG   0.005   0.001   ARG A 360 

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 36
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.9581 (m) cc_final: 0.9337 (p)
REVERT: B  267 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8518 (mmtt)
REVERT: B  298 ILE cc_start: 0.9062 (pt) cc_final: 0.8836 (tt)
REVERT: B  365 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8401 (tm-30)
REVERT: C  371 ILE cc_start: 0.7655 (mm) cc_final: 0.7120 (mp)
REVERT: C  412 TYR cc_start: 0.9055 (m-80) cc_final: 0.8797 (m-80)
  outliers start: 17
  outliers final: 10
  residues processed: 48
  average time/residue: 0.1451
  time to fit residues: 10.3587
Evaluate side-chains
  43 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 32
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  393 PHE
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  434 PHE
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain C residue  267 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 36 optimal weight:    9.9990
   chunk 60 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   chunk 24 optimal weight:    0.6980
   chunk 54 optimal weight:    8.9990
   chunk 44 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 19 optimal weight:   30.0000
   chunk 8 optimal weight:   10.0000
   overall best weight:    3.7186

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.042079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.033802 restraints weight = 39077.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.034982 restraints weight = 23444.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.035807 restraints weight = 16297.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.5930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5034  Z= 0.198
  Angle     :  0.642  15.281   6879  Z= 0.313
  Chirality :  0.042   0.137    798
  Planarity :  0.004   0.055    897
  Dihedral  :  5.543  47.609    711
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.86 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 16.39 %
    Favored  : 80.66 %
  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: -0.47 (0.33), residues: 648
  helix:  1.03 (0.45), residues: 135
  sheet:  0.21 (0.37), residues: 210
  loop : -1.31 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 361 
 HIS   0.003   0.001   HIS A 310 
 PHE   0.018   0.001   PHE A 434 
 TYR   0.025   0.002   TYR A 387 
 ARG   0.003   0.000   ARG B 376 

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 35
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.9599 (m) cc_final: 0.9363 (p)
REVERT: B  267 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8564 (mmtt)
REVERT: B  298 ILE cc_start: 0.9058 (pt) cc_final: 0.8837 (tt)
REVERT: B  365 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8375 (tm-30)
REVERT: C  371 ILE cc_start: 0.7571 (mm) cc_final: 0.7008 (mp)
REVERT: C  412 TYR cc_start: 0.9035 (m-80) cc_final: 0.8797 (m-80)
  outliers start: 16
  outliers final: 10
  residues processed: 45
  average time/residue: 0.1785
  time to fit residues: 11.3983
Evaluate side-chains
  45 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 34
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  393 PHE
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain C residue  265 SER
Chi-restraints excluded: chain C residue  267 LYS
Chi-restraints excluded: chain C residue  287 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 40 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 36 optimal weight:    0.3980
   chunk 10 optimal weight:   30.0000
   chunk 23 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    5.0788

-------------------------------------------------------------------------------
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 = 0.3241 r_free = 0.3241 target = 0.040742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.032692 restraints weight = 39751.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.033836 restraints weight = 23871.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.034640 restraints weight = 16559.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.6363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5034  Z= 0.231
  Angle     :  0.639  12.836   6879  Z= 0.320
  Chirality :  0.043   0.236    798
  Planarity :  0.004   0.060    897
  Dihedral  :  5.351  49.757    709
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 16.25
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.71 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 16.94 %
    Favored  : 79.74 %
  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 (0.33), residues: 648
  helix:  0.97 (0.45), residues: 135
  sheet:  0.14 (0.37), residues: 207
  loop : -1.26 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 361 
 HIS   0.003   0.001   HIS A 310 
 PHE   0.015   0.002   PHE B 321 
 TYR   0.018   0.002   TYR A 387 
 ARG   0.004   0.000   ARG C 407 

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 34
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  267 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8486 (mmtt)
REVERT: C  412 TYR cc_start: 0.9081 (m-80) cc_final: 0.8809 (m-80)
  outliers start: 18
  outliers final: 13
  residues processed: 46
  average time/residue: 0.1686
  time to fit residues: 10.8955
Evaluate side-chains
  41 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 27
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  393 PHE
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain C residue  265 SER
Chi-restraints excluded: chain C residue  267 LYS
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  370 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 51 optimal weight:   20.0000
   chunk 32 optimal weight:    0.1980
   chunk 36 optimal weight:    3.9990
   chunk 16 optimal weight:    7.9990
   chunk 50 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    2.1986

-------------------------------------------------------------------------------
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 = 0.3272 r_free = 0.3272 target = 0.042493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.033865 restraints weight = 40308.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.035023 restraints weight = 24978.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.035860 restraints weight = 17735.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.6507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5034  Z= 0.162
  Angle     :  0.634  12.878   6879  Z= 0.311
  Chirality :  0.043   0.155    798
  Planarity :  0.003   0.055    897
  Dihedral  :  5.103  45.981    709
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.48 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.05 %
    Favored  : 79.56 %
  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: -0.37 (0.33), residues: 648
  helix:  1.07 (0.45), residues: 135
  sheet:  0.29 (0.37), residues: 206
  loop : -1.23 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 421 
 HIS   0.002   0.001   HIS A 310 
 PHE   0.012   0.001   PHE B 321 
 TYR   0.021   0.002   TYR A 387 
 ARG   0.003   0.000   ARG B 376 

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 32
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.9618 (m) cc_final: 0.9402 (p)
REVERT: B  267 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8588 (mmtt)
REVERT: B  365 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8169 (tm-30)
REVERT: C  371 ILE cc_start: 0.7536 (mm) cc_final: 0.6953 (mp)
REVERT: C  412 TYR cc_start: 0.9044 (m-80) cc_final: 0.8762 (m-80)
  outliers start: 13
  outliers final: 11
  residues processed: 41
  average time/residue: 0.1403
  time to fit residues: 8.2395
Evaluate side-chains
  41 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 29
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain C residue  265 SER
Chi-restraints excluded: chain C residue  267 LYS
Chi-restraints excluded: chain C residue  287 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 61 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 39 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   chunk 14 optimal weight:    8.9990
   chunk 13 optimal weight:    8.9990
   chunk 28 optimal weight:    0.0970
   chunk 37 optimal weight:   20.0000
   chunk 9 optimal weight:   10.0000
   overall best weight:    4.2186

-------------------------------------------------------------------------------
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 = 0.3218 r_free = 0.3218 target = 0.040174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.032018 restraints weight = 39679.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.033174 restraints weight = 23863.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.033970 restraints weight = 16610.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.6775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5034  Z= 0.204
  Angle     :  0.637  12.189   6879  Z= 0.316
  Chirality :  0.042   0.165    798
  Planarity :  0.004   0.068    897
  Dihedral  :  5.071  45.273    709
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.40 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 18.23 %
    Favored  : 79.01 %
  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 (0.33), residues: 648
  helix:  0.93 (0.45), residues: 135
  sheet:  0.34 (0.36), residues: 206
  loop : -1.24 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 421 
 HIS   0.003   0.001   HIS A 310 
 PHE   0.012   0.001   PHE B 321 
 TYR   0.019   0.002   TYR A 387 
 ARG   0.003   0.000   ARG B 376 

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 31
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  267 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8650 (mmtt)
REVERT: B  365 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8139 (tm-30)
REVERT: C  412 TYR cc_start: 0.9012 (m-80) cc_final: 0.8643 (m-10)
  outliers start: 15
  outliers final: 13
  residues processed: 41
  average time/residue: 0.1639
  time to fit residues: 10.0382
Evaluate side-chains
  43 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 29
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  393 PHE
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain C residue  265 SER
Chi-restraints excluded: chain C residue  267 LYS
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  370 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 40 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 49 optimal weight:    8.9990
   chunk 33 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 26 optimal weight:   30.0000
   chunk 35 optimal weight:    8.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.039281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.031239 restraints weight = 40194.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.032374 restraints weight = 23894.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.033191 restraints weight = 16544.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.7198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5034  Z= 0.228
  Angle     :  0.634  12.452   6879  Z= 0.319
  Chirality :  0.043   0.150    798
  Planarity :  0.004   0.052    897
  Dihedral  :  5.090  41.618    709
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 15.11
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.56 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 18.42 %
    Favored  : 79.01 %
  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: -0.55 (0.33), residues: 648
  helix:  0.64 (0.44), residues: 135
  sheet:  0.30 (0.37), residues: 206
  loop : -1.30 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 352 
 HIS   0.003   0.001   HIS A 310 
 PHE   0.013   0.002   PHE B 321 
 TYR   0.021   0.002   TYR A 387 
 ARG   0.007   0.000   ARG A 407 

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 33
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  267 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8771 (mmtt)
REVERT: B  365 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8164 (tm-30)
REVERT: C  412 TYR cc_start: 0.9081 (m-80) cc_final: 0.8704 (m-80)
  outliers start: 14
  outliers final: 11
  residues processed: 42
  average time/residue: 0.1771
  time to fit residues: 10.9977
Evaluate side-chains
  42 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 30
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  393 PHE
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain C residue  265 SER
Chi-restraints excluded: chain C residue  267 LYS
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  370 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 33 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 62 optimal weight:   10.0000
   chunk 14 optimal weight:   30.0000
   chunk 10 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   chunk 37 optimal weight:   20.0000
   chunk 48 optimal weight:    5.9990
   chunk 58 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.038380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.030605 restraints weight = 40605.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.031722 restraints weight = 23921.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.032510 restraints weight = 16468.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.7546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5034  Z= 0.254
  Angle     :  0.656  12.524   6879  Z= 0.330
  Chirality :  0.043   0.135    798
  Planarity :  0.004   0.057    897
  Dihedral  :  5.213  45.543    709
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 16.97
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.02 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 18.23 %
    Favored  : 79.19 %
  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: -0.65 (0.33), residues: 648
  helix:  0.55 (0.44), residues: 135
  sheet:  0.14 (0.35), residues: 220
  loop : -1.33 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 352 
 HIS   0.004   0.001   HIS A 310 
 PHE   0.014   0.002   PHE B 321 
 TYR   0.017   0.002   TYR A 387 
 ARG   0.003   0.000   ARG B 376 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1928.74 seconds
wall clock time: 36 minutes 2.31 seconds (2162.31 seconds total)