Starting phenix.real_space_refine
on Tue Feb 11 09:09:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ke9_37150/02_2025/8ke9_37150_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ke9_37150/02_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_37150/02_2025/8ke9_37150.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ke9_37150/02_2025/8ke9_37150.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ke9_37150/02_2025/8ke9_37150_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ke9_37150/02_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-5592/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: 3.24, per 1000 atoms: 0.66
  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: 1.04
  Conformation dependent library (CDL) restraints added in 571.6 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: 0.81
  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: 1.45

  Time building geometry restraints manager: 1.23 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:             0.410
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.000
  Find NCS groups from input model:        0.170
  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:             0.000
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.580
-------------------------------------------------------------------------------
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  : 0.542 
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: 0.2022
  time to fit residues: 28.6681
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  : 0.612 
-------------------------------------------------------------------------------
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 = 0.047434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.038521 restraints weight = 38776.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.039696 restraints weight = 25245.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.040587 restraints weight = 18339.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
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  : 0.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 GLU cc_start: 0.8677 (tt0) cc_final: 0.8136 (tt0)
REVERT: A  389 ASP cc_start: 0.7452 (t0) cc_final: 0.6572 (t0)
REVERT: C  412 TYR cc_start: 0.8976 (m-80) cc_final: 0.8562 (m-80)
  outliers start: 20
  outliers final: 13
  residues processed: 64
  average time/residue: 0.1682
  time to fit residues: 14.1855
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  : 0.601 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 3 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 40 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 4 optimal weight:    6.9990
   chunk 5 optimal weight:   20.0000
   chunk 47 optimal weight:   20.0000
   chunk 33 optimal weight:   20.0000
   chunk 18 optimal weight:   20.0000
   overall best weight:    6.3990

-------------------------------------------------------------------------------
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 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.043413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.034786 restraints weight = 39255.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.035904 restraints weight = 25129.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.036751 restraints weight = 18086.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.4541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5034  Z= 0.291
  Angle     :  0.685   9.072   6879  Z= 0.353
  Chirality :  0.045   0.195    798
  Planarity :  0.005   0.079    897
  Dihedral  :  6.245  48.043    715
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 16.45
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.17 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 13.26 %
    Favored  : 82.14 %
  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:  0.99 (0.42), residues: 135
  sheet:  0.22 (0.36), residues: 225
  loop : -1.20 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 361 
 HIS   0.003   0.001   HIS C 310 
 PHE   0.020   0.002   PHE A 393 
 TYR   0.012   0.002   TYR A 248 
 ARG   0.008   0.001   ARG B 407 

*********************** 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
  68 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 43
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  263 LEU cc_start: 0.9486 (mt) cc_final: 0.9222 (pp)
REVERT: C  412 TYR cc_start: 0.9011 (m-80) cc_final: 0.8656 (m-80)
  outliers start: 25
  outliers final: 17
  residues processed: 60
  average time/residue: 0.1249
  time to fit residues: 10.7398
Evaluate side-chains
  52 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 35
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
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  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  449 VAL
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:   10.0000
   chunk 11 optimal weight:    0.0970
   chunk 12 optimal weight:    7.9990
   chunk 13 optimal weight:    9.9990
   chunk 57 optimal weight:    6.9990
   chunk 53 optimal weight:    8.9990
   chunk 51 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 55 optimal weight:   40.0000
   chunk 59 optimal weight:    0.9980
   chunk 1 optimal weight:    7.9990
   overall best weight:    4.4184

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

Flipped N/Q/H residues before XYZ refinement:
C 310 HIS
C 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.043478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.034881 restraints weight = 39569.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.036039 restraints weight = 24855.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.036890 restraints weight = 17641.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.5063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5034  Z= 0.222
  Angle     :  0.611   7.521   6879  Z= 0.314
  Chirality :  0.042   0.126    798
  Planarity :  0.004   0.062    897
  Dihedral  :  5.915  48.072    713
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 15.73
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.17 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 14.18 %
    Favored  : 81.03 %
  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: -0.33 (0.33), residues: 648
  helix:  1.22 (0.44), residues: 135
  sheet:  0.22 (0.36), residues: 223
  loop : -1.26 (0.35), residues: 290

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   0.016   0.002   PHE B 321 
 TYR   0.019   0.002   TYR A 417 
 ARG   0.008   0.001   ARG A 360 

*********************** 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
  68 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 42
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.9588 (m) cc_final: 0.9336 (p)
REVERT: A  461 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8683 (mp)
REVERT: B  263 LEU cc_start: 0.9483 (mt) cc_final: 0.9257 (pp)
REVERT: B  267 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8572 (mmtt)
REVERT: B  365 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8309 (tm-30)
REVERT: B  415 PHE cc_start: 0.9306 (m-10) cc_final: 0.9076 (m-80)
REVERT: C  267 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8679 (mmmt)
REVERT: C  365 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7534 (mm-30)
REVERT: C  371 ILE cc_start: 0.7560 (mm) cc_final: 0.7065 (mp)
REVERT: C  412 TYR cc_start: 0.9009 (m-80) cc_final: 0.8723 (m-80)
  outliers start: 26
  outliers final: 15
  residues processed: 60
  average time/residue: 0.1391
  time to fit residues: 11.6101
Evaluate side-chains
  58 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 40
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
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  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  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  267 LYS
Chi-restraints excluded: chain B residue  282 ASN
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  447 TYR
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:   20.0000
   chunk 32 optimal weight:    9.9990
   chunk 52 optimal weight:   20.0000
   chunk 48 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 33 optimal weight:    6.9990
   chunk 39 optimal weight:    8.9990
   chunk 8 optimal weight:    8.9990
   chunk 53 optimal weight:    8.9990
   chunk 3 optimal weight:    9.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 403 ASN
C 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.041012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.032715 restraints weight = 40521.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.033797 restraints weight = 25329.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.034638 restraints weight = 17974.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
moved from start:          0.5712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5034  Z= 0.301
  Angle     :  0.673  13.917   6879  Z= 0.337
  Chirality :  0.043   0.142    798
  Planarity :  0.004   0.067    897
  Dihedral  :  6.031  49.970    713
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 17.28
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.79 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 15.10 %
    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: -0.55 (0.33), residues: 648
  helix:  1.03 (0.44), residues: 135
  sheet:  0.14 (0.36), residues: 206
  loop : -1.37 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 361 
 HIS   0.004   0.001   HIS A 310 
 PHE   0.017   0.002   PHE B 321 
 TYR   0.015   0.002   TYR A 369 
 ARG   0.004   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
  61 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 38
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.9596 (m) cc_final: 0.9366 (p)
REVERT: A  365 GLU cc_start: 0.8621 (tt0) cc_final: 0.8032 (tt0)
REVERT: B  267 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8637 (mmtt)
REVERT: B  365 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8326 (tm-30)
REVERT: C  365 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7592 (mm-30)
REVERT: C  412 TYR cc_start: 0.9087 (m-80) cc_final: 0.8843 (m-80)
  outliers start: 23
  outliers final: 16
  residues processed: 53
  average time/residue: 0.1254
  time to fit residues: 9.4658
Evaluate side-chains
  50 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 33
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
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  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  292 THR
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain C residue  265 SER
Chi-restraints excluded: chain C residue  267 LYS
Chi-restraints excluded: chain C residue  269 ASP
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  370 LEU
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:    0.5980
   chunk 60 optimal weight:   20.0000
   chunk 42 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 54 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 19 optimal weight:    8.9990
   chunk 8 optimal weight:   30.0000
   overall best weight:    4.1188

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

Flipped N/Q/H residues before XYZ refinement:
** A 409 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 = 0.3246 r_free = 0.3246 target = 0.040916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.032557 restraints weight = 40122.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.033713 restraints weight = 24571.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.034533 restraints weight = 17233.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.6100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5034  Z= 0.206
  Angle     :  0.616  11.727   6879  Z= 0.311
  Chirality :  0.043   0.194    798
  Planarity :  0.003   0.056    897
  Dihedral  :  5.568  50.178    711
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.94 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 16.57 %
    Favored  : 79.93 %
  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:  1.19 (0.45), residues: 135
  sheet:  0.11 (0.36), residues: 208
  loop : -1.32 (0.35), residues: 305

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   0.014   0.001   PHE B 321 
 TYR   0.016   0.002   TYR A 387 
 ARG   0.006   0.001   ARG B 407 

*********************** 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
  56 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 37
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.9605 (m) cc_final: 0.9385 (p)
REVERT: A  417 TYR cc_start: 0.6284 (m-10) cc_final: 0.6031 (m-10)
REVERT: B  256 ASP cc_start: 0.9322 (m-30) cc_final: 0.9021 (p0)
REVERT: B  267 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8584 (mmtt)
REVERT: B  365 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8335 (tm-30)
REVERT: C  371 ILE cc_start: 0.7551 (mm) cc_final: 0.6991 (mp)
REVERT: C  412 TYR cc_start: 0.9075 (m-80) cc_final: 0.8834 (m-80)
  outliers start: 19
  outliers final: 11
  residues processed: 48
  average time/residue: 0.1285
  time to fit residues: 8.8609
Evaluate side-chains
  46 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 34
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
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 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  447 TYR
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:   20.0000
   chunk 19 optimal weight:   30.0000
   chunk 35 optimal weight:    4.9990
   chunk 29 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   chunk 3 optimal weight:    9.9990
   chunk 36 optimal weight:    4.9990
   chunk 10 optimal weight:   10.0000
   chunk 23 optimal weight:    6.9990
   chunk 4 optimal weight:    7.9990
   chunk 32 optimal weight:    0.5980
   overall best weight:    5.1188

-------------------------------------------------------------------------------
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 = 0.3234 r_free = 0.3234 target = 0.040312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.032309 restraints weight = 39770.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.033446 restraints weight = 23775.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.034236 restraints weight = 16510.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.6427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5034  Z= 0.237
  Angle     :  0.646  11.755   6879  Z= 0.323
  Chirality :  0.043   0.222    798
  Planarity :  0.004   0.059    897
  Dihedral  :  5.333  50.676    709
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.64 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 17.86 %
    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: -0.50 (0.33), residues: 648
  helix:  1.11 (0.45), residues: 135
  sheet:  0.10 (0.36), residues: 206
  loop : -1.30 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 361 
 HIS   0.004   0.001   HIS A 310 
 PHE   0.014   0.002   PHE B 321 
 TYR   0.016   0.002   TYR A 387 
 ARG   0.003   0.000   ARG B 376 

*********************** 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
  50 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 33
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.9619 (m) cc_final: 0.9411 (p)
REVERT: B  256 ASP cc_start: 0.9349 (m-30) cc_final: 0.9104 (p0)
REVERT: B  267 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8587 (mmtt)
REVERT: C  412 TYR cc_start: 0.9065 (m-80) cc_final: 0.8802 (m-80)
  outliers start: 17
  outliers final: 15
  residues processed: 44
  average time/residue: 0.1236
  time to fit residues: 8.0942
Evaluate side-chains
  45 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 29
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 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  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  344 ASN
Chi-restraints excluded: chain B residue  394 VAL
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:   20.0000
   chunk 51 optimal weight:    9.9990
   chunk 32 optimal weight:    8.9990
   chunk 36 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 50 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   chunk 31 optimal weight:   30.0000
   chunk 11 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    3.9988

-------------------------------------------------------------------------------
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 = 0.3232 r_free = 0.3232 target = 0.040275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.032254 restraints weight = 39690.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.033392 restraints weight = 23562.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.034214 restraints weight = 16352.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.6642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5034  Z= 0.199
  Angle     :  0.628  12.407   6879  Z= 0.314
  Chirality :  0.042   0.203    798
  Planarity :  0.004   0.059    897
  Dihedral  :  5.246  50.840    709
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.09 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 18.23 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.33), residues: 648
  helix:  1.23 (0.44), residues: 135
  sheet:  0.16 (0.36), residues: 206
  loop : -1.29 (0.35), residues: 307

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   0.013   0.001   PHE B 321 
 TYR   0.013   0.002   TYR B 412 
 ARG   0.004   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
  47 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 31
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 SER cc_start: 0.9614 (m) cc_final: 0.9410 (p)
REVERT: A  368 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8912 (p)
REVERT: B  256 ASP cc_start: 0.9365 (m-30) cc_final: 0.9117 (p0)
REVERT: B  267 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8694 (mmtt)
REVERT: B  365 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8190 (tm-30)
REVERT: C  412 TYR cc_start: 0.9040 (m-80) cc_final: 0.8778 (m-80)
  outliers start: 16
  outliers final: 12
  residues processed: 43
  average time/residue: 0.1256
  time to fit residues: 8.1941
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  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  368 THR
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  394 VAL
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 61 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 39 optimal weight:   10.0000
   chunk 22 optimal weight:   20.0000
   chunk 14 optimal weight:    6.9990
   chunk 13 optimal weight:   20.0000
   chunk 28 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    5.5990

-------------------------------------------------------------------------------
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 = 0.3182 r_free = 0.3182 target = 0.038840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.031008 restraints weight = 40078.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.032087 restraints weight = 24144.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.032876 restraints weight = 16760.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.7156

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= 0.248
  Angle     :  0.640  12.639   6879  Z= 0.323
  Chirality :  0.043   0.200    798
  Planarity :  0.004   0.075    897
  Dihedral  :  5.346  53.467    709
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 16.66
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.17 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 17.68 %
    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: -0.61 (0.33), residues: 648
  helix:  0.95 (0.43), residues: 135
  sheet:  0.03 (0.36), residues: 214
  loop : -1.36 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 352 
 HIS   0.004   0.001   HIS A 310 
 PHE   0.015   0.002   PHE A 404 
 TYR   0.014   0.002   TYR C 412 
 ARG   0.003   0.001   ARG B 407 

*********************** 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: 18
    poor density    : 28
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  368 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8886 (p)
REVERT: B  256 ASP cc_start: 0.9293 (m-30) cc_final: 0.8989 (p0)
REVERT: B  365 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8180 (tm-30)
REVERT: C  412 TYR cc_start: 0.9088 (m-80) cc_final: 0.8699 (m-80)
  outliers start: 18
  outliers final: 14
  residues processed: 41
  average time/residue: 0.1233
  time to fit residues: 7.4937
Evaluate side-chains
  42 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 27
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  368 THR
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  412 TYR
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  292 THR
Chi-restraints excluded: chain B residue  344 ASN
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:    3.9990
   chunk 61 optimal weight:    9.9990
   chunk 40 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 49 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 54 optimal weight:    5.9990
   chunk 26 optimal weight:   20.0000
   chunk 35 optimal weight:   10.0000
   overall best weight:    3.1586

-------------------------------------------------------------------------------
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 = 0.3203 r_free = 0.3203 target = 0.039435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.031433 restraints weight = 39724.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.032560 restraints weight = 23695.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.033354 restraints weight = 16425.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.7307

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= 0.172
  Angle     :  0.614  12.947   6879  Z= 0.307
  Chirality :  0.042   0.183    798
  Planarity :  0.004   0.064    897
  Dihedral  :  4.376  38.200    705
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.25 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.68 %
    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: -0.34 (0.34), residues: 648
  helix:  1.23 (0.44), residues: 135
  sheet:  0.24 (0.37), residues: 206
  loop : -1.23 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 361 
 HIS   0.002   0.001   HIS A 310 
 PHE   0.014   0.001   PHE A 404 
 TYR   0.015   0.002   TYR B 248 
 ARG   0.003   0.001   ARG B 376 

********************** 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
  45 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 30
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 LEU cc_start: 0.9667 (OUTLIER) cc_final: 0.9408 (mm)
REVERT: A  256 ASP cc_start: 0.9102 (m-30) cc_final: 0.8889 (p0)
REVERT: A  368 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8900 (p)
REVERT: B  256 ASP cc_start: 0.9306 (m-30) cc_final: 0.8997 (p0)
REVERT: B  365 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8143 (tm-30)
REVERT: C  412 TYR cc_start: 0.9100 (m-80) cc_final: 0.8718 (m-80)
  outliers start: 15
  outliers final: 13
  residues processed: 41
  average time/residue: 0.1135
  time to fit residues: 7.1527
Evaluate side-chains
  42 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 27
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  368 THR
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  412 TYR
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 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:    7.9990
   chunk 33 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 62 optimal weight:    9.9990
   chunk 14 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0970
   chunk 30 optimal weight:    7.9990
   chunk 37 optimal weight:   20.0000
   chunk 48 optimal weight:   10.0000
   chunk 58 optimal weight:   20.0000
   chunk 43 optimal weight:    8.9990
   overall best weight:    6.2186

-------------------------------------------------------------------------------
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 = 0.3154 r_free = 0.3154 target = 0.037960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.030241 restraints weight = 40705.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.031360 restraints weight = 23979.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.032118 restraints weight = 16511.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8665
moved from start:          0.7584

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= 0.266
  Angle     :  0.635  12.383   6879  Z= 0.325
  Chirality :  0.042   0.179    798
  Planarity :  0.004   0.080    897
  Dihedral  :  4.560  40.112    705
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 16.25
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.64 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.86 %
    Favored  : 79.37 %
  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:  1.02 (0.44), residues: 135
  sheet:  0.09 (0.36), residues: 213
  loop : -1.39 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 352 
 HIS   0.004   0.001   HIS A 310 
 PHE   0.015   0.002   PHE A 404 
 TYR   0.014   0.002   TYR C 412 
 ARG   0.004   0.001   ARG A 407 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1678.92 seconds
wall clock time: 31 minutes 14.14 seconds (1874.14 seconds total)