Starting phenix.real_space_refine
on Tue Mar  3 21:49:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6s3k_10092/03_2026/6s3k_10092.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6s3k_10092/03_2026/6s3k_10092.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6s3k_10092/03_2026/6s3k_10092.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6s3k_10092/03_2026/6s3k_10092.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6s3k_10092/03_2026/6s3k_10092.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6s3k_10092/03_2026/6s3k_10092.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.005 sd=   0.093
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: 5
    Type Number    sf(0)   Gaussians
     K       6      8.98       5
     S      34      5.16       5
     C    5906      2.51       5
     N    1436      2.21       5
     O    1520      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8902
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 4448
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 573, 4448
          Classifications: {'peptide': 573}
          Link IDs: {'PTRANS': 25, 'TRANS': 547}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {'  K': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    A
  Time building chain proxies: 3.02, per 1000 atoms: 0.34
  Number of scatterers: 8902
  At special positions: 0
  Unit cell: (67.851, 119.547, 109.854, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     K       6     19.00
     S      34     16.00
     O    1520      8.00
     N    1436      7.00
     C    5906      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: 0.44
  Conformation dependent library (CDL) restraints added in 262.2 milliseconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2136

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 1 sheets defined
      67.6% alpha, 3.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'B' and resid 30 through 38
      removed outlier: 4.955A  pdb=" N   ASP B  36 " --> pdb=" O   MET B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 58
    Processing helix  chain 'B' and resid 62 through 88
    Processing helix  chain 'B' and resid 95 through 101
    Processing helix  chain 'B' and resid 107 through 132
      removed outlier: 3.701A  pdb=" N   GLY B 111 " --> pdb=" O   GLY B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 142
      removed outlier: 4.321A  pdb=" N   ASP B 142 " --> pdb=" O   ALA B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 161
      removed outlier: 3.645A  pdb=" N   ALA B 148 " --> pdb=" O   HIS B 144 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   PHE B 150 " --> pdb=" O   PRO B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 193
      removed outlier: 4.292A  pdb=" N   TYR B 175 " --> pdb=" O   ALA B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 225
    Processing helix  chain 'B' and resid 226 through 229
    Processing helix  chain 'B' and resid 231 through 238
      removed outlier: 3.962A  pdb=" N   ILE B 235 " --> pdb=" O   GLY B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 275
    Processing helix  chain 'B' and resid 284 through 294
      removed outlier: 3.890A  pdb=" N   GLN B 288 " --> pdb=" O   THR B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 331
      removed outlier: 3.782A  pdb=" N   ILE B 303 " --> pdb=" O   PHE B 299 " (cutoff:3.500A)
      Proline residue:  B 323  - end of helix
      removed outlier: 3.564A  pdb=" N   ARG B 331 " --> pdb=" O   PHE B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 342
      removed outlier: 3.753A  pdb=" N   PHE B 339 " --> pdb=" O   PRO B 336 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   VAL B 341 " --> pdb=" O   MET B 338 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ARG B 342 " --> pdb=" O   PHE B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 367
    Processing helix  chain 'B' and resid 372 through 399
      removed outlier: 4.243A  pdb=" N   LEU B 376 " --> pdb=" O   HIS B 372 " (cutoff:3.500A)
      Proline residue:  B 384  - end of helix
      removed outlier: 3.835A  pdb=" N   GLN B 399 " --> pdb=" O   LYS B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 428
      removed outlier: 3.559A  pdb=" N   LYS B 407 " --> pdb=" O   GLY B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 461
      removed outlier: 3.669A  pdb=" N   LEU B 437 " --> pdb=" O   VAL B 433 " (cutoff:3.500A)
      Proline residue:  B 441  - end of helix
    Processing helix  chain 'B' and resid 484 through 498
    Processing helix  chain 'B' and resid 511 through 524
      removed outlier: 3.973A  pdb=" N   LYS B 515 " --> pdb=" O   GLU B 511 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 540 through 553
    Processing helix  chain 'B' and resid 582 through 591
    Processing helix  chain 'A' and resid 30 through 38
      removed outlier: 4.955A  pdb=" N   ASP A  36 " --> pdb=" O   MET A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 58
    Processing helix  chain 'A' and resid 62 through 88
    Processing helix  chain 'A' and resid 95 through 101
    Processing helix  chain 'A' and resid 107 through 132
      removed outlier: 3.700A  pdb=" N   GLY A 111 " --> pdb=" O   GLY A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 141
    Processing helix  chain 'A' and resid 144 through 161
      removed outlier: 3.646A  pdb=" N   ALA A 148 " --> pdb=" O   HIS A 144 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   PHE A 150 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 193
      removed outlier: 4.292A  pdb=" N   TYR A 175 " --> pdb=" O   ALA A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 225
    Processing helix  chain 'A' and resid 226 through 229
    Processing helix  chain 'A' and resid 231 through 238
      removed outlier: 3.962A  pdb=" N   ILE A 235 " --> pdb=" O   GLY A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 275
    Processing helix  chain 'A' and resid 284 through 294
      removed outlier: 3.890A  pdb=" N   GLN A 288 " --> pdb=" O   THR A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 331
      removed outlier: 3.783A  pdb=" N   ILE A 303 " --> pdb=" O   PHE A 299 " (cutoff:3.500A)
      Proline residue:  A 323  - end of helix
      removed outlier: 3.564A  pdb=" N   ARG A 331 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 342
      removed outlier: 3.753A  pdb=" N   PHE A 339 " --> pdb=" O   PRO A 336 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   VAL A 341 " --> pdb=" O   MET A 338 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ARG A 342 " --> pdb=" O   PHE A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 367
    Processing helix  chain 'A' and resid 372 through 399
      removed outlier: 4.244A  pdb=" N   LEU A 376 " --> pdb=" O   HIS A 372 " (cutoff:3.500A)
      Proline residue:  A 384  - end of helix
      removed outlier: 3.836A  pdb=" N   GLN A 399 " --> pdb=" O   LYS A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 428
      removed outlier: 3.559A  pdb=" N   LYS A 407 " --> pdb=" O   GLY A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 461
      removed outlier: 3.669A  pdb=" N   LEU A 437 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
      Proline residue:  A 441  - end of helix
    Processing helix  chain 'A' and resid 484 through 498
    Processing helix  chain 'A' and resid 511 through 524
      removed outlier: 3.972A  pdb=" N   LYS A 515 " --> pdb=" O   GLU A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 553
    Processing helix  chain 'A' and resid 582 through 591
    Processing sheet with id=AA1, first strand: chain 'B' and resid 502 through 503
      removed outlier: 8.423A  pdb=" N   ILE B 502 " --> pdb=" O   THR B 474 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   VAL B 476 " --> pdb=" O   ILE B 502 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   VAL B 475 " --> pdb=" O   MET B 562 " (cutoff:3.500A)
      removed outlier: 7.287A  pdb=" N   LEU B 564 " --> pdb=" O   VAL B 475 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   ILE B 477 " --> pdb=" O   LEU B 564 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   MET B 597 " --> pdb=" O   VAL B 561 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   MET A 597 " --> pdb=" O   VAL A 561 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   VAL A 475 " --> pdb=" O   MET A 562 " (cutoff:3.500A)
      removed outlier: 7.287A  pdb=" N   LEU A 564 " --> pdb=" O   VAL A 475 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   ILE A 477 " --> pdb=" O   LEU A 564 " (cutoff:3.500A)
      removed outlier: 8.422A  pdb=" N   ILE A 502 " --> pdb=" O   THR A 474 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   VAL A 476 " --> pdb=" O   ILE A 502 " (cutoff:3.500A)

    558 hydrogen bonds defined for protein.
    1650 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: 1.26

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2583
        1.34 -     1.46: 1572
        1.46 -     1.57: 4889
        1.57 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 9106
  Sorted by residual:
  bond pdb=" C   ILE B 239 "
       pdb=" N   PRO B 240 "
    ideal  model  delta    sigma   weight residual
    1.334  1.402 -0.068 2.34e-02 1.83e+03 8.39e+00
  bond pdb=" C   ILE A 239 "
       pdb=" N   PRO A 240 "
    ideal  model  delta    sigma   weight residual
    1.334  1.401 -0.067 2.34e-02 1.83e+03 8.23e+00
  bond pdb=" C   VAL A 145 "
       pdb=" N   PRO A 146 "
    ideal  model  delta    sigma   weight residual
    1.334  1.374 -0.040 2.34e-02 1.83e+03 2.94e+00
  bond pdb=" CG  LEU B 120 "
       pdb=" CD1 LEU B 120 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.91e+00
  bond pdb=" C   VAL B 145 "
       pdb=" N   PRO B 146 "
    ideal  model  delta    sigma   weight residual
    1.334  1.374 -0.040 2.34e-02 1.83e+03 2.91e+00
  ... (remaining 9101 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.83: 12004
        2.83 -     5.66: 324
        5.66 -     8.49: 44
        8.49 -    11.31: 4
       11.31 -    14.14: 6
  Bond angle restraints: 12382
  Sorted by residual:
  angle pdb=" C   PHE B 508 "
        pdb=" N   ASP B 509 "
        pdb=" CA  ASP B 509 "
      ideal   model   delta    sigma   weight residual
     123.91  131.06   -7.15 1.66e+00 3.63e-01 1.85e+01
  angle pdb=" C   PHE A 508 "
        pdb=" N   ASP A 509 "
        pdb=" CA  ASP A 509 "
      ideal   model   delta    sigma   weight residual
     123.91  131.06   -7.15 1.66e+00 3.63e-01 1.85e+01
  angle pdb=" C   MET B 193 "
        pdb=" N   THR B 194 "
        pdb=" CA  THR B 194 "
      ideal   model   delta    sigma   weight residual
     121.54  129.75   -8.21 1.91e+00 2.74e-01 1.85e+01
  angle pdb=" C   MET A 193 "
        pdb=" N   THR A 194 "
        pdb=" CA  THR A 194 "
      ideal   model   delta    sigma   weight residual
     121.54  129.69   -8.15 1.91e+00 2.74e-01 1.82e+01
  angle pdb=" CA  LEU A 461 "
        pdb=" CB  LEU A 461 "
        pdb=" CG  LEU A 461 "
      ideal   model   delta    sigma   weight residual
     116.30  130.44  -14.14 3.50e+00 8.16e-02 1.63e+01
  ... (remaining 12377 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.82: 4680
       16.82 -    33.64: 528
       33.64 -    50.46: 120
       50.46 -    67.28: 14
       67.28 -    84.10: 14
  Dihedral angle restraints: 5356
    sinusoidal: 2042
      harmonic: 3314
  Sorted by residual:
  dihedral pdb=" CA  PHE B 382 "
           pdb=" C   PHE B 382 "
           pdb=" N   ILE B 383 "
           pdb=" CA  ILE B 383 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.82   26.18     0      5.00e+00 4.00e-02 2.74e+01
  dihedral pdb=" CA  PHE A 382 "
           pdb=" C   PHE A 382 "
           pdb=" N   ILE A 383 "
           pdb=" CA  ILE A 383 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.83   26.17     0      5.00e+00 4.00e-02 2.74e+01
  dihedral pdb=" CA  LYS A 105 "
           pdb=" C   LYS A 105 "
           pdb=" N   PRO A 106 "
           pdb=" CA  PRO A 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.58   24.42     0      5.00e+00 4.00e-02 2.39e+01
  ... (remaining 5353 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 944
       0.050 -    0.101: 379
       0.101 -    0.151: 130
       0.151 -    0.201: 28
       0.201 -    0.251: 11
  Chirality restraints: 1492
  Sorted by residual:
  chirality pdb=" CA  ASP A 509 "
            pdb=" N   ASP A 509 "
            pdb=" C   ASP A 509 "
            pdb=" CB  ASP A 509 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CA  ASP B 509 "
            pdb=" N   ASP B 509 "
            pdb=" C   ASP B 509 "
            pdb=" CB  ASP B 509 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" CB  ILE B 239 "
            pdb=" CA  ILE B 239 "
            pdb=" CG1 ILE B 239 "
            pdb=" CG2 ILE B 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.40e+00
  ... (remaining 1489 not shown)

  Planarity restraints: 1508
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 434 "    0.048 5.00e-02 4.00e+02   7.13e-02 8.12e+00
        pdb=" N   PRO A 435 "   -0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO A 435 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 435 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B 434 "   -0.048 5.00e-02 4.00e+02   7.12e-02 8.11e+00
        pdb=" N   PRO B 435 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO B 435 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 435 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 335 "   -0.045 5.00e-02 4.00e+02   6.86e-02 7.53e+00
        pdb=" N   PRO B 336 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO B 336 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 336 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 1505 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.85: 3024
        2.85 -     3.42: 9854
        3.42 -     3.99: 15718
        3.99 -     4.57: 21472
        4.57 -     5.14: 31348
  Nonbonded interactions: 81416
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 507 "
            pdb=" O   LEU B 532 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OG  SER A 507 "
            pdb=" O   LEU A 532 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OH  TYR A  88 "
            pdb=" OE2 GLU A 100 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OH  TYR B  88 "
            pdb=" OE2 GLU B 100 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OG  SER B  80 "
            pdb=" OE1 GLN B 389 "
     model   vdw
     2.309 3.040
  ... (remaining 81411 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 'B'
  selection = chain 'A'
}

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:             0.590
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.120
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  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:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
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      :  0.008   0.079   9106  Z= 0.330
  Angle     :  1.124  14.143  12382  Z= 0.594
  Chirality :  0.063   0.251   1492
  Planarity :  0.009   0.071   1508
  Dihedral  : 15.380  84.105   3220
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.67 %
    Favored  : 89.33 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 12.29 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.54 (0.19), residues: 1134
  helix: -2.35 (0.14), residues: 748
  sheet: -2.40 (0.57), residues: 66
  loop : -4.38 (0.28), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 161 
 TYR   0.030   0.003   TYR A 377 
 PHE   0.020   0.002   PHE A 299 
 TRP   0.021   0.002   TRP B 520 
 HIS   0.004   0.002   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00777 ( 9106)
  covalent geometry    : angle       1.12362 (12382)
  hydrogen bonds       : bond        0.12610 (  558)
  hydrogen bonds       : angle       5.74911 ( 1650)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 172
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   32 MET cc_start: 0.5486 (mtt) cc_final: 0.5204 (ptp)
REVERT: B   52 LEU cc_start: 0.8590 (tp) cc_final: 0.8333 (tp)
REVERT: B   75 LEU cc_start: 0.8518 (tp) cc_final: 0.8317 (tp)
REVERT: B  229 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8665 (pp)
REVERT: B  294 PHE cc_start: 0.5568 (t80) cc_final: 0.5358 (t80)
REVERT: B  573 ARG cc_start: 0.7709 (ptt180) cc_final: 0.7075 (mmm160)
REVERT: A   32 MET cc_start: 0.5624 (mtt) cc_final: 0.5359 (ptp)
REVERT: A   51 ILE cc_start: 0.7893 (mt) cc_final: 0.7616 (mt)
REVERT: A  229 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8539 (pp)
REVERT: A  393 CYS cc_start: 0.8647 (t) cc_final: 0.8423 (t)
REVERT: A  404 TRP cc_start: 0.7490 (t60) cc_final: 0.7196 (t60)
REVERT: A  551 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7920 (mt-10)
REVERT: A  573 ARG cc_start: 0.7620 (ptt180) cc_final: 0.6988 (mmm160)
  outliers start: 6
  outliers final: 2
  residues processed: 177
  average time/residue: 0.0815
  time to fit residues: 20.4744
Evaluate side-chains
  125 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 121
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  501 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    7.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
B  47 GLN
B 203 HIS
B 316 ASN
B 575 HIS
A  47 GLN
A 203 HIS
A 316 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.169396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.128584 restraints weight = 12865.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.132660 restraints weight = 7694.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.135267 restraints weight = 5607.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.136561 restraints weight = 4621.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.137922 restraints weight = 4137.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9106  Z= 0.143
  Angle     :  0.694   9.381  12382  Z= 0.355
  Chirality :  0.044   0.168   1492
  Planarity :  0.006   0.054   1508
  Dihedral  :  5.625  31.063   1216
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 17.60 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.90 (0.24), residues: 1134
  helix: -0.17 (0.18), residues: 756
  sheet: -1.16 (0.71), residues: 48
  loop : -3.83 (0.30), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 337 
 TYR   0.018   0.002   TYR B 377 
 PHE   0.019   0.001   PHE A 448 
 TRP   0.027   0.002   TRP A 520 
 HIS   0.003   0.001   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9106)
  covalent geometry    : angle       0.69395 (12382)
  hydrogen bonds       : bond        0.04773 (  558)
  hydrogen bonds       : angle       4.43676 ( 1650)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 146
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   32 MET cc_start: 0.5601 (mtt) cc_final: 0.5318 (ptp)
REVERT: B  229 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8477 (pp)
REVERT: B  573 ARG cc_start: 0.7449 (ptt180) cc_final: 0.7082 (mmm160)
REVERT: B  579 HIS cc_start: 0.7580 (OUTLIER) cc_final: 0.6454 (t-90)
REVERT: A   32 MET cc_start: 0.5748 (mtt) cc_final: 0.5491 (ptp)
REVERT: A   51 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7243 (mt)
REVERT: A  229 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8466 (pp)
REVERT: A  440 MET cc_start: 0.7827 (tpp) cc_final: 0.7209 (mmt)
REVERT: A  573 ARG cc_start: 0.7422 (ptt180) cc_final: 0.7092 (mmm160)
REVERT: A  579 HIS cc_start: 0.7476 (OUTLIER) cc_final: 0.7126 (m-70)
  outliers start: 26
  outliers final: 12
  residues processed: 163
  average time/residue: 0.0712
  time to fit residues: 17.4469
Evaluate side-chains
  147 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  563 VAL
Chi-restraints excluded: chain B residue  579 HIS
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  533 HIS
Chi-restraints excluded: chain A residue  579 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 6 optimal weight:    0.0670
   chunk 1 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 88 optimal weight:    0.0970
   chunk 57 optimal weight:    9.9990
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.5116

-------------------------------------------------------------------------------
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 = 0.4180 r_free = 0.4180 target = 0.172402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.132165 restraints weight = 12892.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.136305 restraints weight = 7591.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.139095 restraints weight = 5507.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.140586 restraints weight = 4496.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.141827 restraints weight = 3991.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9106  Z= 0.128
  Angle     :  0.653  10.999  12382  Z= 0.329
  Chirality :  0.043   0.173   1492
  Planarity :  0.005   0.047   1508
  Dihedral  :  5.054  23.239   1216
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 20.83 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.25), residues: 1134
  helix:  0.67 (0.19), residues: 752
  sheet: -0.24 (0.80), residues: 46
  loop : -3.44 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 248 
 TYR   0.014   0.001   TYR B 377 
 PHE   0.019   0.001   PHE A 448 
 TRP   0.018   0.002   TRP A 520 
 HIS   0.002   0.000   HIS A 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 9106)
  covalent geometry    : angle       0.65308 (12382)
  hydrogen bonds       : bond        0.04227 (  558)
  hydrogen bonds       : angle       4.15581 ( 1650)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 141
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   32 MET cc_start: 0.5601 (mtt) cc_final: 0.5308 (ptp)
REVERT: B   51 ILE cc_start: 0.7290 (OUTLIER) cc_final: 0.6974 (mt)
REVERT: B   52 LEU cc_start: 0.8014 (tp) cc_final: 0.7723 (tp)
REVERT: B  229 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8409 (pp)
REVERT: B  440 MET cc_start: 0.7883 (tpt) cc_final: 0.7576 (tpp)
REVERT: B  573 ARG cc_start: 0.7403 (ptt180) cc_final: 0.7066 (mmm160)
REVERT: B  579 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.6260 (t-90)
REVERT: A   32 MET cc_start: 0.5587 (mtt) cc_final: 0.5320 (ptp)
REVERT: A  229 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8384 (pp)
REVERT: A  292 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.5758 (mp0)
REVERT: A  440 MET cc_start: 0.7741 (tpp) cc_final: 0.7239 (mmt)
REVERT: A  573 ARG cc_start: 0.7407 (ptt180) cc_final: 0.7071 (mmm160)
REVERT: A  579 HIS cc_start: 0.7498 (OUTLIER) cc_final: 0.5954 (t-90)
  outliers start: 29
  outliers final: 12
  residues processed: 161
  average time/residue: 0.0690
  time to fit residues: 16.8136
Evaluate side-chains
  152 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  324 GLN
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  579 HIS
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  300 TYR
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  579 HIS
Chi-restraints excluded: chain A residue  598 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 70 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 108 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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 = 0.4175 r_free = 0.4175 target = 0.171824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.131871 restraints weight = 13179.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.136069 restraints weight = 7664.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.138790 restraints weight = 5521.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.140524 restraints weight = 4508.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.141428 restraints weight = 3971.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.2484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9106  Z= 0.130
  Angle     :  0.655   9.745  12382  Z= 0.325
  Chirality :  0.043   0.160   1492
  Planarity :  0.005   0.045   1508
  Dihedral  :  4.783  22.591   1214
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 21.25 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.26), residues: 1134
  helix:  1.06 (0.19), residues: 752
  sheet:  0.19 (0.84), residues: 46
  loop : -3.31 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  82 
 TYR   0.014   0.001   TYR B 377 
 PHE   0.021   0.001   PHE B 448 
 TRP   0.028   0.002   TRP A 520 
 HIS   0.001   0.000   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 9106)
  covalent geometry    : angle       0.65484 (12382)
  hydrogen bonds       : bond        0.04137 (  558)
  hydrogen bonds       : angle       3.98623 ( 1650)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 137
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   32 MET cc_start: 0.5665 (mtt) cc_final: 0.5370 (ptp)
REVERT: B   52 LEU cc_start: 0.8016 (tp) cc_final: 0.7779 (tp)
REVERT: B  229 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8350 (pp)
REVERT: B  440 MET cc_start: 0.7951 (tpt) cc_final: 0.7578 (tpp)
REVERT: B  573 ARG cc_start: 0.7425 (ptt180) cc_final: 0.6440 (tmt170)
REVERT: B  579 HIS cc_start: 0.7504 (OUTLIER) cc_final: 0.6601 (t-90)
REVERT: A   32 MET cc_start: 0.5687 (mtt) cc_final: 0.5387 (ptp)
REVERT: A   51 ILE cc_start: 0.7184 (OUTLIER) cc_final: 0.6877 (mt)
REVERT: A  229 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8312 (pp)
REVERT: A  408 MET cc_start: 0.7904 (tmm) cc_final: 0.7389 (tmm)
REVERT: A  440 MET cc_start: 0.7785 (tpp) cc_final: 0.7225 (mmt)
REVERT: A  573 ARG cc_start: 0.7339 (ptt180) cc_final: 0.7044 (mmm160)
REVERT: A  579 HIS cc_start: 0.7485 (OUTLIER) cc_final: 0.6287 (t-90)
  outliers start: 36
  outliers final: 19
  residues processed: 165
  average time/residue: 0.0712
  time to fit residues: 17.6868
Evaluate side-chains
  151 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  324 GLN
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  579 HIS
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  300 TYR
Chi-restraints excluded: chain A residue  324 GLN
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  562 MET
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  579 HIS
Chi-restraints excluded: chain A residue  597 MET
Chi-restraints excluded: chain A residue  598 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 45 optimal weight:    0.4980
   chunk 66 optimal weight:    0.5980
   chunk 87 optimal weight:    5.9990
   chunk 101 optimal weight:    7.9990
   chunk 91 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 90 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4177 r_free = 0.4177 target = 0.172336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.133117 restraints weight = 13012.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.137325 restraints weight = 7573.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.140110 restraints weight = 5422.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.141785 restraints weight = 4402.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.142335 restraints weight = 3861.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9106  Z= 0.126
  Angle     :  0.643   9.417  12382  Z= 0.320
  Chirality :  0.043   0.157   1492
  Planarity :  0.005   0.045   1508
  Dihedral  :  4.625  22.308   1214
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 22.81 %
    Favored  : 73.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.26), residues: 1134
  helix:  1.26 (0.19), residues: 758
  sheet:  0.38 (0.85), residues: 46
  loop : -3.14 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 519 
 TYR   0.012   0.001   TYR A 377 
 PHE   0.022   0.001   PHE B 448 
 TRP   0.021   0.001   TRP A 520 
 HIS   0.001   0.000   HIS A 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 9106)
  covalent geometry    : angle       0.64322 (12382)
  hydrogen bonds       : bond        0.04016 (  558)
  hydrogen bonds       : angle       3.90381 ( 1650)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 140
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   32 MET cc_start: 0.5603 (mtt) cc_final: 0.5374 (ptp)
REVERT: B   52 LEU cc_start: 0.7924 (tp) cc_final: 0.7712 (tp)
REVERT: B  133 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.7951 (tp)
REVERT: B  229 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8392 (pp)
REVERT: B  335 MET cc_start: 0.7633 (mmm) cc_final: 0.6610 (mtp)
REVERT: B  440 MET cc_start: 0.7820 (tpt) cc_final: 0.7423 (tpp)
REVERT: B  445 LEU cc_start: 0.7856 (tt) cc_final: 0.7652 (tp)
REVERT: B  448 PHE cc_start: 0.6618 (t80) cc_final: 0.6385 (t80)
REVERT: B  573 ARG cc_start: 0.7403 (ptt180) cc_final: 0.6434 (tmt170)
REVERT: B  579 HIS cc_start: 0.7445 (OUTLIER) cc_final: 0.6638 (t-90)
REVERT: A   32 MET cc_start: 0.5685 (mtt) cc_final: 0.5461 (ptp)
REVERT: A  143 TYR cc_start: 0.7327 (p90) cc_final: 0.7101 (p90)
REVERT: A  229 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8319 (pp)
REVERT: A  292 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.5666 (mp0)
REVERT: A  440 MET cc_start: 0.7738 (tpp) cc_final: 0.7182 (mmt)
REVERT: A  520 TRP cc_start: 0.7030 (t60) cc_final: 0.6821 (t60)
REVERT: A  573 ARG cc_start: 0.7346 (ptt180) cc_final: 0.6948 (mmm160)
REVERT: A  579 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.6325 (t-90)
  outliers start: 39
  outliers final: 23
  residues processed: 169
  average time/residue: 0.0649
  time to fit residues: 16.6476
Evaluate side-chains
  161 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 132
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  324 GLN
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  579 HIS
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  300 TYR
Chi-restraints excluded: chain A residue  324 GLN
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  533 HIS
Chi-restraints excluded: chain A residue  562 MET
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  579 HIS
Chi-restraints excluded: chain A residue  597 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 83 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   chunk 3 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9990
   chunk 60 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9980
   chunk 71 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 558 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.169138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.129207 restraints weight = 13226.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.133393 restraints weight = 7724.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.136096 restraints weight = 5560.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.137804 restraints weight = 4532.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.138547 restraints weight = 3992.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9106  Z= 0.150
  Angle     :  0.679   9.501  12382  Z= 0.337
  Chirality :  0.044   0.155   1492
  Planarity :  0.005   0.047   1508
  Dihedral  :  4.628  22.156   1214
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 23.96 %
    Favored  : 71.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.26), residues: 1134
  helix:  1.29 (0.19), residues: 754
  sheet:  0.45 (0.84), residues: 46
  loop : -3.13 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  82 
 TYR   0.016   0.001   TYR A 377 
 PHE   0.019   0.001   PHE B 448 
 TRP   0.027   0.002   TRP B 520 
 HIS   0.002   0.001   HIS B 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 9106)
  covalent geometry    : angle       0.67922 (12382)
  hydrogen bonds       : bond        0.04296 (  558)
  hydrogen bonds       : angle       3.91316 ( 1650)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 137
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   32 MET cc_start: 0.5666 (mtt) cc_final: 0.5449 (ptp)
REVERT: B   51 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.7062 (mt)
REVERT: B   52 LEU cc_start: 0.8210 (tp) cc_final: 0.7920 (tp)
REVERT: B  133 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.7984 (tp)
REVERT: B  229 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8400 (pp)
REVERT: B  259 ILE cc_start: 0.7902 (tt) cc_final: 0.7573 (tp)
REVERT: B  335 MET cc_start: 0.7692 (mmm) cc_final: 0.6701 (mtp)
REVERT: B  440 MET cc_start: 0.7913 (tpt) cc_final: 0.7489 (tpp)
REVERT: B  448 PHE cc_start: 0.6664 (t80) cc_final: 0.6389 (t80)
REVERT: B  573 ARG cc_start: 0.7324 (ptt180) cc_final: 0.6421 (tmt170)
REVERT: B  579 HIS cc_start: 0.7516 (OUTLIER) cc_final: 0.6549 (t-90)
REVERT: A   32 MET cc_start: 0.5676 (mtt) cc_final: 0.5458 (ptp)
REVERT: A   51 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.7015 (mt)
REVERT: A  133 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8087 (tp)
REVERT: A  143 TYR cc_start: 0.7337 (p90) cc_final: 0.7131 (p90)
REVERT: A  189 LEU cc_start: 0.8074 (mt) cc_final: 0.6931 (pp)
REVERT: A  229 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8393 (pp)
REVERT: A  292 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.5795 (mp0)
REVERT: A  335 MET cc_start: 0.7545 (mmm) cc_final: 0.6569 (mtp)
REVERT: A  440 MET cc_start: 0.7729 (tpp) cc_final: 0.7124 (mmt)
REVERT: A  573 ARG cc_start: 0.7354 (ptt180) cc_final: 0.6952 (mmm160)
REVERT: A  579 HIS cc_start: 0.7447 (OUTLIER) cc_final: 0.6451 (t-90)
  outliers start: 45
  outliers final: 28
  residues processed: 172
  average time/residue: 0.0711
  time to fit residues: 18.3762
Evaluate side-chains
  170 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 133
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  324 GLN
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  579 HIS
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  300 TYR
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  579 HIS
Chi-restraints excluded: chain A residue  597 MET
Chi-restraints excluded: chain A residue  598 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 90 optimal weight:    0.8980
   chunk 94 optimal weight:    0.0770
   chunk 104 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9980
   overall best weight:    1.1942

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

Flipped N/Q/H residues before XYZ refinement:
A 558 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.170179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.130400 restraints weight = 13232.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.134603 restraints weight = 7722.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.137259 restraints weight = 5561.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.138572 restraints weight = 4554.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.139873 restraints weight = 4063.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.2838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9106  Z= 0.140
  Angle     :  0.670   9.336  12382  Z= 0.332
  Chirality :  0.044   0.155   1492
  Planarity :  0.005   0.047   1508
  Dihedral  :  4.589  21.866   1214
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 24.48 %
    Favored  : 70.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.26), residues: 1134
  helix:  1.29 (0.19), residues: 764
  sheet:  0.50 (0.84), residues: 46
  loop : -3.12 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  82 
 TYR   0.015   0.001   TYR A 377 
 PHE   0.017   0.001   PHE B 448 
 TRP   0.028   0.002   TRP A 520 
 HIS   0.002   0.001   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 9106)
  covalent geometry    : angle       0.67045 (12382)
  hydrogen bonds       : bond        0.04204 (  558)
  hydrogen bonds       : angle       3.91998 ( 1650)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 137
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   51 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.7081 (mt)
REVERT: B   52 LEU cc_start: 0.8231 (tp) cc_final: 0.7934 (tp)
REVERT: B  133 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8021 (tp)
REVERT: B  229 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8381 (pp)
REVERT: B  259 ILE cc_start: 0.7885 (tt) cc_final: 0.7551 (tp)
REVERT: B  335 MET cc_start: 0.7673 (mmm) cc_final: 0.6679 (mtp)
REVERT: B  440 MET cc_start: 0.7881 (tpt) cc_final: 0.7460 (tpp)
REVERT: B  448 PHE cc_start: 0.6719 (t80) cc_final: 0.6497 (t80)
REVERT: B  573 ARG cc_start: 0.7353 (ptt180) cc_final: 0.6438 (tmt170)
REVERT: B  579 HIS cc_start: 0.7530 (OUTLIER) cc_final: 0.6525 (t-90)
REVERT: A   51 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.7016 (mt)
REVERT: A  133 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8040 (tp)
REVERT: A  143 TYR cc_start: 0.7298 (p90) cc_final: 0.7077 (p90)
REVERT: A  189 LEU cc_start: 0.8060 (mt) cc_final: 0.6993 (pp)
REVERT: A  229 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8398 (pp)
REVERT: A  292 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.5760 (mp0)
REVERT: A  335 MET cc_start: 0.7529 (mmm) cc_final: 0.6546 (mtp)
REVERT: A  440 MET cc_start: 0.7734 (tpp) cc_final: 0.7127 (mmt)
REVERT: A  573 ARG cc_start: 0.7345 (ptt180) cc_final: 0.6955 (mmm160)
REVERT: A  579 HIS cc_start: 0.7417 (OUTLIER) cc_final: 0.6450 (t-90)
  outliers start: 45
  outliers final: 31
  residues processed: 172
  average time/residue: 0.0664
  time to fit residues: 17.5593
Evaluate side-chains
  170 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 130
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  324 GLN
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  579 HIS
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  300 TYR
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  533 HIS
Chi-restraints excluded: chain A residue  562 MET
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  579 HIS
Chi-restraints excluded: chain A residue  597 MET
Chi-restraints excluded: chain A residue  598 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 112 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 109 optimal weight:    0.1980
   chunk 100 optimal weight:    2.9990
   chunk 53 optimal weight:   10.0000
   chunk 20 optimal weight:    0.6980
   chunk 1 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.4164 r_free = 0.4164 target = 0.171250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.131588 restraints weight = 13225.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.135842 restraints weight = 7712.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.138508 restraints weight = 5538.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.140005 restraints weight = 4517.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.140539 restraints weight = 4009.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.3001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9106  Z= 0.130
  Angle     :  0.658  13.356  12382  Z= 0.323
  Chirality :  0.043   0.199   1492
  Planarity :  0.005   0.046   1508
  Dihedral  :  4.509  21.673   1214
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 25.42 %
    Favored  : 70.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.26), residues: 1134
  helix:  1.38 (0.19), residues: 762
  sheet:  0.55 (0.84), residues: 46
  loop : -3.06 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 462 
 TYR   0.014   0.001   TYR A  95 
 PHE   0.020   0.001   PHE A 448 
 TRP   0.032   0.002   TRP B 520 
 HIS   0.002   0.000   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9106)
  covalent geometry    : angle       0.65772 (12382)
  hydrogen bonds       : bond        0.04030 (  558)
  hydrogen bonds       : angle       3.88419 ( 1650)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 138
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 LEU cc_start: 0.8217 (tp) cc_final: 0.7975 (tp)
REVERT: B  133 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8012 (tp)
REVERT: B  229 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8346 (pp)
REVERT: B  259 ILE cc_start: 0.7860 (tt) cc_final: 0.7523 (tp)
REVERT: B  335 MET cc_start: 0.7619 (mmm) cc_final: 0.6597 (mtp)
REVERT: B  440 MET cc_start: 0.7877 (tpt) cc_final: 0.7446 (tpp)
REVERT: B  445 LEU cc_start: 0.7800 (tt) cc_final: 0.7571 (tp)
REVERT: B  573 ARG cc_start: 0.7371 (ptt180) cc_final: 0.6395 (tmt170)
REVERT: B  579 HIS cc_start: 0.7512 (OUTLIER) cc_final: 0.6576 (t-90)
REVERT: A  133 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8021 (tp)
REVERT: A  143 TYR cc_start: 0.7283 (p90) cc_final: 0.7014 (p90)
REVERT: A  189 LEU cc_start: 0.8059 (mt) cc_final: 0.7058 (pp)
REVERT: A  229 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8388 (pp)
REVERT: A  292 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.5705 (mp0)
REVERT: A  440 MET cc_start: 0.7689 (tpp) cc_final: 0.7113 (mmt)
REVERT: A  573 ARG cc_start: 0.7342 (ptt180) cc_final: 0.6945 (mmm160)
REVERT: A  579 HIS cc_start: 0.7372 (OUTLIER) cc_final: 0.6379 (t-90)
  outliers start: 41
  outliers final: 29
  residues processed: 168
  average time/residue: 0.0675
  time to fit residues: 17.2540
Evaluate side-chains
  170 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 134
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  324 GLN
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  579 HIS
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  300 TYR
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  533 HIS
Chi-restraints excluded: chain A residue  562 MET
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  579 HIS
Chi-restraints excluded: chain A residue  597 MET
Chi-restraints excluded: chain A residue  598 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 71 optimal weight:    6.9990
   chunk 58 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 112 optimal weight:    0.9980
   chunk 111 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 558 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.170632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.130918 restraints weight = 13203.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.135076 restraints weight = 7721.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.137777 restraints weight = 5545.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.138875 restraints weight = 4532.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.140241 restraints weight = 4085.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9106  Z= 0.136
  Angle     :  0.662  12.327  12382  Z= 0.325
  Chirality :  0.044   0.189   1492
  Planarity :  0.005   0.047   1508
  Dihedral  :  4.491  21.769   1214
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 26.15 %
    Favored  : 69.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.26), residues: 1134
  helix:  1.34 (0.19), residues: 772
  sheet:  0.67 (0.84), residues: 46
  loop : -3.36 (0.31), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 161 
 TYR   0.015   0.001   TYR B 377 
 PHE   0.023   0.001   PHE A 448 
 TRP   0.029   0.002   TRP A 520 
 HIS   0.002   0.001   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9106)
  covalent geometry    : angle       0.66233 (12382)
  hydrogen bonds       : bond        0.04091 (  558)
  hydrogen bonds       : angle       3.87113 ( 1650)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 141
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: B   51 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.7030 (mt)
REVERT: B   52 LEU cc_start: 0.8232 (tp) cc_final: 0.7924 (tp)
REVERT: B  133 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8016 (tp)
REVERT: B  229 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8340 (pp)
REVERT: B  259 ILE cc_start: 0.7870 (tt) cc_final: 0.7531 (tp)
REVERT: B  335 MET cc_start: 0.7665 (mmm) cc_final: 0.6719 (mtp)
REVERT: B  440 MET cc_start: 0.7845 (tpt) cc_final: 0.7372 (tpp)
REVERT: B  445 LEU cc_start: 0.7807 (tt) cc_final: 0.7565 (tp)
REVERT: B  573 ARG cc_start: 0.7365 (ptt180) cc_final: 0.6407 (tmt170)
REVERT: B  579 HIS cc_start: 0.7534 (OUTLIER) cc_final: 0.6610 (t-90)
REVERT: A   51 ILE cc_start: 0.7274 (OUTLIER) cc_final: 0.6960 (mt)
REVERT: A  143 TYR cc_start: 0.7310 (p90) cc_final: 0.7063 (p90)
REVERT: A  229 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8405 (pp)
REVERT: A  259 ILE cc_start: 0.7847 (tt) cc_final: 0.7489 (tp)
REVERT: A  292 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.5634 (mp0)
REVERT: A  335 MET cc_start: 0.7532 (mmm) cc_final: 0.6504 (mtp)
REVERT: A  440 MET cc_start: 0.7698 (tpp) cc_final: 0.7099 (mmt)
REVERT: A  573 ARG cc_start: 0.7331 (ptt180) cc_final: 0.6952 (mmm160)
REVERT: A  579 HIS cc_start: 0.7368 (OUTLIER) cc_final: 0.6388 (t-90)
  outliers start: 41
  outliers final: 30
  residues processed: 173
  average time/residue: 0.0629
  time to fit residues: 16.5155
Evaluate side-chains
  173 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 135
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  324 GLN
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  579 HIS
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  300 TYR
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  533 HIS
Chi-restraints excluded: chain A residue  562 MET
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  579 HIS
Chi-restraints excluded: chain A residue  597 MET
Chi-restraints excluded: chain A residue  598 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 107 optimal weight:   10.0000
   chunk 74 optimal weight:    6.9990
   chunk 111 optimal weight:   10.0000
   chunk 44 optimal weight:    0.2980
   chunk 21 optimal weight:    0.4980
   chunk 3 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 102 optimal weight:    0.0040
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.5594

-------------------------------------------------------------------------------
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 = 0.4182 r_free = 0.4182 target = 0.174383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.134254 restraints weight = 12999.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.138320 restraints weight = 7633.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.140918 restraints weight = 5494.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.142529 restraints weight = 4491.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.143070 restraints weight = 3965.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9106  Z= 0.123
  Angle     :  0.648  12.375  12382  Z= 0.318
  Chirality :  0.043   0.183   1492
  Planarity :  0.005   0.046   1508
  Dihedral  :  4.393  21.736   1214
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 25.94 %
    Favored  : 69.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.27), residues: 1134
  helix:  1.50 (0.20), residues: 760
  sheet:  0.74 (0.84), residues: 46
  loop : -3.04 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 519 
 TYR   0.012   0.001   TYR A 377 
 PHE   0.022   0.001   PHE A 448 
 TRP   0.044   0.002   TRP A 520 
 HIS   0.002   0.000   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9106)
  covalent geometry    : angle       0.64800 (12382)
  hydrogen bonds       : bond        0.03887 (  558)
  hydrogen bonds       : angle       3.86012 ( 1650)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 138
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: B  133 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.7955 (tp)
REVERT: B  229 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8391 (pp)
REVERT: B  259 ILE cc_start: 0.7809 (tt) cc_final: 0.7473 (tp)
REVERT: B  335 MET cc_start: 0.7660 (mmm) cc_final: 0.6648 (mtp)
REVERT: B  404 TRP cc_start: 0.6541 (t60) cc_final: 0.6338 (t60)
REVERT: B  440 MET cc_start: 0.7804 (tpt) cc_final: 0.7551 (tpp)
REVERT: B  520 TRP cc_start: 0.7194 (t60) cc_final: 0.6967 (t60)
REVERT: B  573 ARG cc_start: 0.7386 (ptt180) cc_final: 0.6421 (tmt170)
REVERT: B  579 HIS cc_start: 0.7441 (OUTLIER) cc_final: 0.6513 (t-90)
REVERT: A   51 ILE cc_start: 0.7176 (OUTLIER) cc_final: 0.6865 (mt)
REVERT: A  133 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.7942 (tp)
REVERT: A  229 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8438 (pp)
REVERT: A  292 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.5488 (mp0)
REVERT: A  335 MET cc_start: 0.7547 (mmm) cc_final: 0.6457 (mtp)
REVERT: A  404 TRP cc_start: 0.6701 (t60) cc_final: 0.6490 (t60)
REVERT: A  440 MET cc_start: 0.7594 (tpp) cc_final: 0.7004 (mmt)
REVERT: A  543 PHE cc_start: 0.7800 (t80) cc_final: 0.6837 (t80)
REVERT: A  573 ARG cc_start: 0.7349 (ptt180) cc_final: 0.6927 (mmm160)
REVERT: A  579 HIS cc_start: 0.7313 (OUTLIER) cc_final: 0.6129 (t-90)
  outliers start: 42
  outliers final: 27
  residues processed: 169
  average time/residue: 0.0689
  time to fit residues: 17.5099
Evaluate side-chains
  168 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 133
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  324 GLN
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  579 HIS
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  300 TYR
Chi-restraints excluded: chain A residue  324 GLN
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  533 HIS
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  579 HIS
Chi-restraints excluded: chain A residue  598 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 1 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 109 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.3980
   chunk 39 optimal weight:    0.9980
   chunk 100 optimal weight:    6.9990
   chunk 104 optimal weight:    8.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.4025 r_free = 0.4025 target = 0.162172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.121974 restraints weight = 12682.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.126286 restraints weight = 7329.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.129274 restraints weight = 5185.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.131118 restraints weight = 4170.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.131876 restraints weight = 3619.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.3290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9106  Z= 0.130
  Angle     :  0.658  11.959  12382  Z= 0.324
  Chirality :  0.043   0.178   1492
  Planarity :  0.005   0.049   1508
  Dihedral  :  4.411  21.594   1214
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 26.77 %
    Favored  : 69.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.26), residues: 1134
  helix:  1.38 (0.19), residues: 772
  sheet:  0.79 (0.84), residues: 46
  loop : -3.30 (0.31), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 587 
 TYR   0.013   0.001   TYR A 377 
 PHE   0.024   0.001   PHE B 448 
 TRP   0.038   0.002   TRP A 520 
 HIS   0.002   0.000   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9106)
  covalent geometry    : angle       0.65762 (12382)
  hydrogen bonds       : bond        0.03969 (  558)
  hydrogen bonds       : angle       3.86020 ( 1650)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1358.19 seconds
wall clock time: 24 minutes 14.11 seconds (1454.11 seconds total)