Starting phenix.real_space_refine
on Thu Jul 24 23:48:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zat_39888/07_2025/8zat_39888.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zat_39888/07_2025/8zat_39888.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zat_39888/07_2025/8zat_39888.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zat_39888/07_2025/8zat_39888.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zat_39888/07_2025/8zat_39888.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zat_39888/07_2025/8zat_39888.cif"
  }
  resolution = 3.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    4528      2.51       5
     N    1110      2.21       5
     O    1126      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6800
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3400
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 440, 3400
          Classifications: {'peptide': 440}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 23, 'TRANS': 416}
          Chain breaks: 4
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 32
          Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "B"
      Number of atoms: 3400
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 440, 3400
          Classifications: {'peptide': 440}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 23, 'TRANS': 416}
          Chain breaks: 4
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 32
          Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 24
  Time building chain proxies: 5.01, per 1000 atoms: 0.74
  Number of scatterers: 6800
  At special positions: 0
  Unit cell: (128.65, 88.81, 81.34, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1126      8.00
     N    1110      7.00
     C    4528      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 157 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 526 " - pdb=" SG  CYS A 536 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 157 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 526 " - pdb=" SG  CYS B 536 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.71
  Conformation dependent library (CDL) restraints added in 985.5 milliseconds
  

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1624

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 0 sheets defined
      85.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 63
    Processing helix  chain 'A' and resid 74 through 98
      removed outlier: 3.547A  pdb=" N   VAL A  78 " --> pdb=" O   ARG A  74 " (cutoff:3.500A)
      Proline residue:  A  88  - end of helix
    Processing helix  chain 'A' and resid 100 through 123
      removed outlier: 3.595A  pdb=" N   VAL A 104 " --> pdb=" O   ARG A 100 " (cutoff:3.500A)
      Proline residue:  A 119  - end of helix
    Processing helix  chain 'A' and resid 123 through 132
      removed outlier: 3.638A  pdb=" N   ARG A 127 " --> pdb=" O   PHE A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 191
    Processing helix  chain 'A' and resid 191 through 224
      removed outlier: 3.867A  pdb=" N   ILE A 224 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 247
      Proline residue:  A 233  - end of helix
    Processing helix  chain 'A' and resid 304 through 322
      removed outlier: 3.610A  pdb=" N   LYS A 315 " --> pdb=" O   GLN A 311 " (cutoff:3.500A)
      Proline residue:  A 318  - end of helix
    Processing helix  chain 'A' and resid 322 through 343
      removed outlier: 4.087A  pdb=" N   TYR A 326 " --> pdb=" O   THR A 322 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   SER A 335 " --> pdb=" O   PHE A 331 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   VAL A 338 " --> pdb=" O   GLN A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 401
      removed outlier: 3.713A  pdb=" N   LEU A 377 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   VAL A 383 " --> pdb=" O   ASN A 379 " (cutoff:3.500A)
      Proline residue:  A 388  - end of helix
      removed outlier: 4.443A  pdb=" N   ASP A 395 " --> pdb=" O   ASP A 391 " (cutoff:3.500A)
      Proline residue:  A 396  - end of helix
    Processing helix  chain 'A' and resid 408 through 439
    Processing helix  chain 'A' and resid 457 through 460
    Processing helix  chain 'A' and resid 461 through 484
      removed outlier: 3.598A  pdb=" N   ILE A 477 " --> pdb=" O   ILE A 473 " (cutoff:3.500A)
      Proline residue:  A 478  - end of helix
    Processing helix  chain 'A' and resid 491 through 519
      removed outlier: 3.609A  pdb=" N   MET A 496 " --> pdb=" O   GLN A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 532
    Processing helix  chain 'A' and resid 537 through 564
    Processing helix  chain 'B' and resid 30 through 63
    Processing helix  chain 'B' and resid 74 through 98
      removed outlier: 3.545A  pdb=" N   VAL B  78 " --> pdb=" O   ARG B  74 " (cutoff:3.500A)
      Proline residue:  B  88  - end of helix
    Processing helix  chain 'B' and resid 100 through 123
      removed outlier: 3.599A  pdb=" N   VAL B 104 " --> pdb=" O   ARG B 100 " (cutoff:3.500A)
      Proline residue:  B 119  - end of helix
    Processing helix  chain 'B' and resid 123 through 132
      removed outlier: 3.642A  pdb=" N   ARG B 127 " --> pdb=" O   PHE B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 191
    Processing helix  chain 'B' and resid 191 through 224
      removed outlier: 3.861A  pdb=" N   ILE B 224 " --> pdb=" O   ILE B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 247
      Proline residue:  B 233  - end of helix
    Processing helix  chain 'B' and resid 304 through 322
      removed outlier: 3.598A  pdb=" N   LYS B 315 " --> pdb=" O   GLN B 311 " (cutoff:3.500A)
      Proline residue:  B 318  - end of helix
    Processing helix  chain 'B' and resid 322 through 343
      removed outlier: 4.085A  pdb=" N   TYR B 326 " --> pdb=" O   THR B 322 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   SER B 335 " --> pdb=" O   PHE B 331 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   VAL B 338 " --> pdb=" O   GLN B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 401
      removed outlier: 3.712A  pdb=" N   LEU B 377 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   VAL B 383 " --> pdb=" O   ASN B 379 " (cutoff:3.500A)
      Proline residue:  B 388  - end of helix
      removed outlier: 4.487A  pdb=" N   ASP B 395 " --> pdb=" O   ASP B 391 " (cutoff:3.500A)
      Proline residue:  B 396  - end of helix
    Processing helix  chain 'B' and resid 408 through 439
    Processing helix  chain 'B' and resid 457 through 460
    Processing helix  chain 'B' and resid 461 through 484
      removed outlier: 3.601A  pdb=" N   ILE B 477 " --> pdb=" O   ILE B 473 " (cutoff:3.500A)
      Proline residue:  B 478  - end of helix
    Processing helix  chain 'B' and resid 491 through 519
      removed outlier: 3.600A  pdb=" N   MET B 496 " --> pdb=" O   GLN B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 532
    Processing helix  chain 'B' and resid 537 through 564

    560 hydrogen bonds defined for protein.
    1656 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: 1.94

  Time building geometry restraints manager: 2.03 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2080
        1.35 -     1.47: 1818
        1.47 -     1.60: 3026
        1.60 -     1.72: 0
        1.72 -     1.84: 58
  Bond restraints: 6982
  Sorted by residual:
  bond pdb=" C   ALA B 487 "
       pdb=" N   PRO B 488 "
    ideal  model  delta    sigma   weight residual
    1.334  1.378 -0.045 2.34e-02 1.83e+03 3.62e+00
  bond pdb=" C   ALA A 487 "
       pdb=" N   PRO A 488 "
    ideal  model  delta    sigma   weight residual
    1.334  1.378 -0.044 2.34e-02 1.83e+03 3.49e+00
  bond pdb=" CA  ILE B 462 "
       pdb=" C   ILE B 462 "
    ideal  model  delta    sigma   weight residual
    1.520  1.529 -0.009 8.80e-03 1.29e+04 1.04e+00
  bond pdb=" CB  CYS A 157 "
       pdb=" SG  CYS A 157 "
    ideal  model  delta    sigma   weight residual
    1.808  1.839 -0.031 3.30e-02 9.18e+02 9.08e-01
  bond pdb=" CA  VAL A 387 "
       pdb=" C   VAL A 387 "
    ideal  model  delta    sigma   weight residual
    1.520  1.528 -0.008 8.80e-03 1.29e+04 9.07e-01
  ... (remaining 6977 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 9356
        1.95 -     3.91: 112
        3.91 -     5.86: 37
        5.86 -     7.82: 13
        7.82 -     9.77: 4
  Bond angle restraints: 9522
  Sorted by residual:
  angle pdb=" N   PRO B 351 "
        pdb=" CA  PRO B 351 "
        pdb=" CB  PRO B 351 "
      ideal   model   delta    sigma   weight residual
     103.00  110.47   -7.47 1.10e+00 8.26e-01 4.61e+01
  angle pdb=" N   PRO A 351 "
        pdb=" CA  PRO A 351 "
        pdb=" CB  PRO A 351 "
      ideal   model   delta    sigma   weight residual
     103.00  110.46   -7.46 1.10e+00 8.26e-01 4.60e+01
  angle pdb=" N   ALA A 487 "
        pdb=" CA  ALA A 487 "
        pdb=" C   ALA A 487 "
      ideal   model   delta    sigma   weight residual
     109.81  118.80   -8.99 2.21e+00 2.05e-01 1.66e+01
  angle pdb=" N   ALA B 487 "
        pdb=" CA  ALA B 487 "
        pdb=" C   ALA B 487 "
      ideal   model   delta    sigma   weight residual
     109.81  118.78   -8.97 2.21e+00 2.05e-01 1.65e+01
  angle pdb=" C   GLN B 461 "
        pdb=" N   ILE B 462 "
        pdb=" CA  ILE B 462 "
      ideal   model   delta    sigma   weight residual
     120.24  122.50   -2.26 6.30e-01 2.52e+00 1.29e+01
  ... (remaining 9517 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.69: 3474
       14.69 -    29.38: 381
       29.38 -    44.08: 145
       44.08 -    58.77: 30
       58.77 -    73.46: 6
  Dihedral angle restraints: 4036
    sinusoidal: 1510
      harmonic: 2526
  Sorted by residual:
  dihedral pdb=" CA  ALA B 487 "
           pdb=" C   ALA B 487 "
           pdb=" N   PRO B 488 "
           pdb=" CA  PRO B 488 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -142.43  -37.57     0      5.00e+00 4.00e-02 5.64e+01
  dihedral pdb=" CA  ALA A 487 "
           pdb=" C   ALA A 487 "
           pdb=" N   PRO A 488 "
           pdb=" CA  PRO A 488 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -142.63  -37.37     0      5.00e+00 4.00e-02 5.59e+01
  dihedral pdb=" CB  CYS B 131 "
           pdb=" SG  CYS B 131 "
           pdb=" SG  CYS B 157 "
           pdb=" CB  CYS B 157 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -24.73  -61.27     1      1.00e+01 1.00e-02 4.99e+01
  ... (remaining 4033 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 905
       0.049 -    0.099: 174
       0.099 -    0.148: 29
       0.148 -    0.197: 0
       0.197 -    0.246: 2
  Chirality restraints: 1110
  Sorted by residual:
  chirality pdb=" CA  PRO B 351 "
            pdb=" N   PRO B 351 "
            pdb=" C   PRO B 351 "
            pdb=" CB  PRO B 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" CA  PRO A 351 "
            pdb=" N   PRO A 351 "
            pdb=" C   PRO A 351 "
            pdb=" CB  PRO A 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.48    0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  CYS A 131 "
            pdb=" N   CYS A 131 "
            pdb=" C   CYS A 131 "
            pdb=" CB  CYS A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.33e-01
  ... (remaining 1107 not shown)

  Planarity restraints: 1172
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 487 "   -0.039 5.00e-02 4.00e+02   5.89e-02 5.56e+00
        pdb=" N   PRO B 488 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO B 488 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 488 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 487 "    0.038 5.00e-02 4.00e+02   5.87e-02 5.52e+00
        pdb=" N   PRO A 488 "   -0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO A 488 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 488 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B  74 "    0.008 2.00e-02 2.50e+03   1.59e-02 2.52e+00
        pdb=" C   ARG B  74 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   ARG B  74 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ALA B  75 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1169 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 794
        2.75 -     3.29: 7240
        3.29 -     3.82: 12118
        3.82 -     4.36: 12868
        4.36 -     4.90: 22047
  Nonbonded interactions: 55067
  Sorted by model distance:
  nonbonded pdb=" O   PHE A  65 "
            pdb=" N   THR A  68 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" O   PHE B  65 "
            pdb=" N   THR B  68 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" OH  TYR B 203 "
            pdb=" OE2 GLU B 472 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OH  TYR A 203 "
            pdb=" OE2 GLU A 472 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   GLN B 332 "
            pdb=" OG1 THR B 336 "
     model   vdw
     2.251 3.040
  ... (remaining 55062 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             4.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.990
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5910
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6986  Z= 0.144
  Angle     :  0.686   9.770   9530  Z= 0.369
  Chirality :  0.040   0.246   1110
  Planarity :  0.005   0.059   1172
  Dihedral  : 14.573  73.459   2400
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 18.66 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.30), residues: 860
  helix:  1.56 (0.20), residues: 714
  sheet:  None (None), residues: 0
  loop : -3.16 (0.48), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  67 
 HIS   0.001   0.000   HIS A 434 
 PHE   0.008   0.001   PHE B  65 
 TYR   0.010   0.001   TYR B  59 
 ARG   0.002   0.000   ARG B 432 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11369 (  560)
  hydrogen bonds       : angle       5.17285 ( 1656)
  SS BOND              : bond        0.00229 (    4)
  SS BOND              : angle       2.33298 (    8)
  covalent geometry    : bond        0.00280 ( 6982)
  covalent geometry    : angle       0.68298 ( 9522)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 226
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ARG cc_start: 0.5579 (tmt170) cc_final: 0.4682 (tmm160)
REVERT: A   83 SER cc_start: 0.7421 (t) cc_final: 0.7106 (p)
REVERT: A  309 ASN cc_start: 0.6766 (m110) cc_final: 0.6558 (m110)
REVERT: B   74 ARG cc_start: 0.5600 (tmt170) cc_final: 0.4699 (tmm160)
REVERT: B   83 SER cc_start: 0.7400 (t) cc_final: 0.7091 (p)
REVERT: B  309 ASN cc_start: 0.6750 (m110) cc_final: 0.6503 (m110)
  outliers start: 2
  outliers final: 2
  residues processed: 228
  average time/residue: 0.2078
  time to fit residues: 60.6890
Evaluate side-chains
  152 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 150
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 GLN
Chi-restraints excluded: chain B residue  332 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 44 optimal weight:    9.9990
   chunk 35 optimal weight:    0.4980
   chunk 68 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 334 GLN
** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5027 r_free = 0.5027 target = 0.246476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4749 r_free = 0.4749 target = 0.218063 restraints weight = 11710.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4786 r_free = 0.4786 target = 0.221960 restraints weight = 7540.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4809 r_free = 0.4809 target = 0.224406 restraints weight = 5771.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.4829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6118
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6986  Z= 0.187
  Angle     :  0.798   9.386   9530  Z= 0.387
  Chirality :  0.046   0.242   1110
  Planarity :  0.006   0.066   1172
  Dihedral  :  5.522  43.974    946
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 16.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 22.08 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.30), residues: 860
  helix:  1.32 (0.20), residues: 734
  sheet:  None (None), residues: 0
  loop : -3.53 (0.47), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  92 
 HIS   0.005   0.001   HIS B 525 
 PHE   0.020   0.002   PHE B 416 
 TYR   0.016   0.002   TYR A 484 
 ARG   0.003   0.001   ARG B 432 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04576 (  560)
  hydrogen bonds       : angle       4.68631 ( 1656)
  SS BOND              : bond        0.00196 (    4)
  SS BOND              : angle       0.97954 (    8)
  covalent geometry    : bond        0.00405 ( 6982)
  covalent geometry    : angle       0.79780 ( 9522)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 156
  time to evaluate  : 0.647 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 THR cc_start: 0.5138 (OUTLIER) cc_final: 0.4735 (p)
REVERT: A   74 ARG cc_start: 0.5590 (tmt170) cc_final: 0.4677 (tmm160)
REVERT: A   83 SER cc_start: 0.7127 (t) cc_final: 0.6730 (p)
REVERT: A  317 LEU cc_start: 0.5890 (OUTLIER) cc_final: 0.5348 (mt)
REVERT: A  333 MET cc_start: 0.5774 (mtp) cc_final: 0.4832 (ttm)
REVERT: B   73 THR cc_start: 0.5211 (OUTLIER) cc_final: 0.4786 (p)
REVERT: B   74 ARG cc_start: 0.5644 (tmt170) cc_final: 0.4741 (tmm160)
REVERT: B   83 SER cc_start: 0.7130 (t) cc_final: 0.6751 (p)
REVERT: B  317 LEU cc_start: 0.5876 (OUTLIER) cc_final: 0.5221 (mt)
REVERT: B  333 MET cc_start: 0.5787 (mtp) cc_final: 0.4833 (ttm)
  outliers start: 21
  outliers final: 8
  residues processed: 166
  average time/residue: 0.1836
  time to fit residues: 40.3567
Evaluate side-chains
  148 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  421 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0770
   chunk 29 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0870
   chunk 65 optimal weight:    5.9990
   chunk 85 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 76 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    0.8120

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

Flipped N/Q/H residues before XYZ refinement:
** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5010 r_free = 0.5010 target = 0.244025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4768 r_free = 0.4768 target = 0.217941 restraints weight = 11824.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4759 r_free = 0.4759 target = 0.218421 restraints weight = 9028.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4765 r_free = 0.4765 target = 0.218970 restraints weight = 7999.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.4775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6245
moved from start:          0.3168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6986  Z= 0.189
  Angle     :  0.790   8.426   9530  Z= 0.387
  Chirality :  0.046   0.261   1110
  Planarity :  0.006   0.062   1172
  Dihedral  :  5.011  36.808    940
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 17.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 22.36 %
    Favored  : 72.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.30), residues: 860
  helix:  1.21 (0.20), residues: 734
  sheet:  None (None), residues: 0
  loop : -3.32 (0.52), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  92 
 HIS   0.005   0.001   HIS A 525 
 PHE   0.017   0.002   PHE B 416 
 TYR   0.017   0.002   TYR A 484 
 ARG   0.004   0.000   ARG B 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04464 (  560)
  hydrogen bonds       : angle       4.69841 ( 1656)
  SS BOND              : bond        0.01130 (    4)
  SS BOND              : angle       0.69215 (    8)
  covalent geometry    : bond        0.00414 ( 6982)
  covalent geometry    : angle       0.78967 ( 9522)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 141
  time to evaluate  : 0.678 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 THR cc_start: 0.5095 (OUTLIER) cc_final: 0.4685 (p)
REVERT: A   74 ARG cc_start: 0.5675 (tmt170) cc_final: 0.4746 (tmm160)
REVERT: A   83 SER cc_start: 0.7100 (t) cc_final: 0.6752 (p)
REVERT: A  317 LEU cc_start: 0.5825 (OUTLIER) cc_final: 0.5154 (mt)
REVERT: B   73 THR cc_start: 0.5219 (OUTLIER) cc_final: 0.4775 (p)
REVERT: B   74 ARG cc_start: 0.5770 (tmt170) cc_final: 0.4827 (tmm160)
REVERT: B   83 SER cc_start: 0.7092 (t) cc_final: 0.6721 (p)
REVERT: B  182 PHE cc_start: 0.5979 (OUTLIER) cc_final: 0.5649 (t80)
REVERT: B  317 LEU cc_start: 0.5765 (OUTLIER) cc_final: 0.4984 (mt)
  outliers start: 35
  outliers final: 14
  residues processed: 158
  average time/residue: 0.1958
  time to fit residues: 41.0288
Evaluate side-chains
  148 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 PHE
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain B residue   50 PHE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  383 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 70 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0170
   chunk 46 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   chunk 43 optimal weight:    0.4980
   chunk 63 optimal weight:    0.9980
   chunk 72 optimal weight:    0.0010
   overall best weight:    0.3424

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 ASN
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5018 r_free = 0.5018 target = 0.244907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.216280 restraints weight = 11789.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4786 r_free = 0.4786 target = 0.220776 restraints weight = 7045.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4813 r_free = 0.4813 target = 0.223608 restraints weight = 5110.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.4833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6105
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6986  Z= 0.163
  Angle     :  0.773   8.313   9530  Z= 0.377
  Chirality :  0.046   0.232   1110
  Planarity :  0.005   0.060   1172
  Dihedral  :  5.058  38.296    940
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 16.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 23.36 %
    Favored  : 73.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.30), residues: 860
  helix:  1.23 (0.20), residues: 732
  sheet:  None (None), residues: 0
  loop : -3.33 (0.51), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  92 
 HIS   0.003   0.001   HIS B 525 
 PHE   0.013   0.001   PHE B 543 
 TYR   0.014   0.002   TYR A 484 
 ARG   0.003   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04118 (  560)
  hydrogen bonds       : angle       4.60522 ( 1656)
  SS BOND              : bond        0.01144 (    4)
  SS BOND              : angle       0.85702 (    8)
  covalent geometry    : bond        0.00336 ( 6982)
  covalent geometry    : angle       0.77312 ( 9522)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 151
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 THR cc_start: 0.5105 (OUTLIER) cc_final: 0.4687 (p)
REVERT: A   74 ARG cc_start: 0.5839 (tmt170) cc_final: 0.4865 (tmm160)
REVERT: A   83 SER cc_start: 0.7069 (t) cc_final: 0.6747 (p)
REVERT: A  182 PHE cc_start: 0.6379 (t80) cc_final: 0.5935 (t80)
REVERT: A  317 LEU cc_start: 0.5665 (OUTLIER) cc_final: 0.4987 (mt)
REVERT: B   73 THR cc_start: 0.5098 (OUTLIER) cc_final: 0.4679 (p)
REVERT: B   74 ARG cc_start: 0.5759 (tmt170) cc_final: 0.4794 (tmm160)
REVERT: B   83 SER cc_start: 0.7085 (t) cc_final: 0.6771 (p)
REVERT: B  182 PHE cc_start: 0.6147 (OUTLIER) cc_final: 0.5682 (t80)
REVERT: B  317 LEU cc_start: 0.5608 (OUTLIER) cc_final: 0.4945 (mt)
  outliers start: 23
  outliers final: 14
  residues processed: 162
  average time/residue: 0.1906
  time to fit residues: 40.3238
Evaluate side-chains
  152 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 PHE
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain B residue   50 PHE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  465 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 309 ASN
** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4996 r_free = 0.4996 target = 0.242216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4739 r_free = 0.4739 target = 0.214827 restraints weight = 11535.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.216294 restraints weight = 7873.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4750 r_free = 0.4750 target = 0.217157 restraints weight = 6452.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.4768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6250
moved from start:          0.3699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6986  Z= 0.181
  Angle     :  0.812   9.071   9530  Z= 0.398
  Chirality :  0.046   0.228   1110
  Planarity :  0.005   0.054   1172
  Dihedral  :  5.017  33.522    940
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 16.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 21.65 %
    Favored  : 72.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.29), residues: 860
  helix:  1.17 (0.20), residues: 718
  sheet:  None (None), residues: 0
  loop : -3.31 (0.45), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  92 
 HIS   0.001   0.000   HIS A 434 
 PHE   0.018   0.002   PHE A  79 
 TYR   0.010   0.002   TYR A 337 
 ARG   0.005   0.000   ARG A 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04342 (  560)
  hydrogen bonds       : angle       4.67913 ( 1656)
  SS BOND              : bond        0.00215 (    4)
  SS BOND              : angle       0.51309 (    8)
  covalent geometry    : bond        0.00398 ( 6982)
  covalent geometry    : angle       0.81208 ( 9522)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 141
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 THR cc_start: 0.5173 (OUTLIER) cc_final: 0.4739 (p)
REVERT: A   74 ARG cc_start: 0.5710 (tmt170) cc_final: 0.5178 (ttp-170)
REVERT: A   83 SER cc_start: 0.7066 (t) cc_final: 0.6703 (p)
REVERT: A  317 LEU cc_start: 0.5864 (OUTLIER) cc_final: 0.5199 (mt)
REVERT: A  333 MET cc_start: 0.6228 (ttm) cc_final: 0.4910 (ttm)
REVERT: B   73 THR cc_start: 0.5131 (OUTLIER) cc_final: 0.4691 (p)
REVERT: B   74 ARG cc_start: 0.5757 (tmt170) cc_final: 0.5197 (ttp-170)
REVERT: B   83 SER cc_start: 0.7113 (t) cc_final: 0.6768 (p)
REVERT: B  182 PHE cc_start: 0.6276 (OUTLIER) cc_final: 0.5648 (t80)
REVERT: B  317 LEU cc_start: 0.5893 (OUTLIER) cc_final: 0.5209 (mt)
  outliers start: 38
  outliers final: 16
  residues processed: 160
  average time/residue: 0.1966
  time to fit residues: 41.2299
Evaluate side-chains
  154 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 PHE
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  465 TYR
Chi-restraints excluded: chain A residue  491 MET
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain B residue   50 PHE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  465 TYR
Chi-restraints excluded: chain B residue  491 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 72 optimal weight:    0.5980
   chunk 85 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 81 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   chunk 21 optimal weight:    8.9990
   chunk 54 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4985 r_free = 0.4985 target = 0.241170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4699 r_free = 0.4699 target = 0.212087 restraints weight = 11710.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4736 r_free = 0.4736 target = 0.216035 restraints weight = 7596.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.4760 r_free = 0.4760 target = 0.218435 restraints weight = 5802.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.4781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6216
moved from start:          0.4027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6986  Z= 0.189
  Angle     :  0.829  11.620   9530  Z= 0.401
  Chirality :  0.046   0.220   1110
  Planarity :  0.005   0.060   1172
  Dihedral  :  5.093  37.914    940
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 16.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 22.36 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.29), residues: 860
  helix:  1.08 (0.19), residues: 714
  sheet:  None (None), residues: 0
  loop : -3.46 (0.44), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  92 
 HIS   0.002   0.000   HIS B 525 
 PHE   0.022   0.002   PHE A  79 
 TYR   0.020   0.002   TYR A 337 
 ARG   0.002   0.000   ARG A 432 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04383 (  560)
  hydrogen bonds       : angle       4.69936 ( 1656)
  SS BOND              : bond        0.00646 (    4)
  SS BOND              : angle       0.59396 (    8)
  covalent geometry    : bond        0.00417 ( 6982)
  covalent geometry    : angle       0.82958 ( 9522)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 141
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 THR cc_start: 0.5183 (OUTLIER) cc_final: 0.4697 (p)
REVERT: A   74 ARG cc_start: 0.5776 (tmt170) cc_final: 0.5226 (ttp-170)
REVERT: A   83 SER cc_start: 0.7191 (t) cc_final: 0.6879 (p)
REVERT: A  182 PHE cc_start: 0.6719 (t80) cc_final: 0.6021 (t80)
REVERT: A  317 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5372 (mt)
REVERT: B   73 THR cc_start: 0.5308 (OUTLIER) cc_final: 0.4834 (p)
REVERT: B   74 ARG cc_start: 0.5712 (tmt170) cc_final: 0.5176 (ttp-170)
REVERT: B   83 SER cc_start: 0.7202 (t) cc_final: 0.6887 (p)
REVERT: B  182 PHE cc_start: 0.6543 (OUTLIER) cc_final: 0.5796 (t80)
REVERT: B  317 LEU cc_start: 0.6047 (OUTLIER) cc_final: 0.5455 (mt)
  outliers start: 32
  outliers final: 17
  residues processed: 157
  average time/residue: 0.1910
  time to fit residues: 39.4259
Evaluate side-chains
  162 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 PHE
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  465 TYR
Chi-restraints excluded: chain A residue  491 MET
Chi-restraints excluded: chain A residue  525 HIS
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain B residue   50 PHE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  465 TYR
Chi-restraints excluded: chain B residue  491 MET
Chi-restraints excluded: chain B residue  539 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 3 optimal weight:    0.4980
   chunk 25 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 74 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0030
   chunk 51 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4991 r_free = 0.4991 target = 0.241959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4730 r_free = 0.4730 target = 0.214226 restraints weight = 11402.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4741 r_free = 0.4741 target = 0.216409 restraints weight = 8314.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4740 r_free = 0.4740 target = 0.217197 restraints weight = 6203.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.4764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6251
moved from start:          0.4189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6986  Z= 0.172
  Angle     :  0.817  10.724   9530  Z= 0.394
  Chirality :  0.046   0.198   1110
  Planarity :  0.005   0.050   1172
  Dihedral  :  5.011  31.376    940
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 23.08 %
    Favored  : 72.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.29), residues: 860
  helix:  1.21 (0.19), residues: 712
  sheet:  None (None), residues: 0
  loop : -3.54 (0.42), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  92 
 HIS   0.004   0.001   HIS B 525 
 PHE   0.026   0.001   PHE A  79 
 TYR   0.010   0.001   TYR A 337 
 ARG   0.003   0.000   ARG B 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04252 (  560)
  hydrogen bonds       : angle       4.65055 ( 1656)
  SS BOND              : bond        0.00244 (    4)
  SS BOND              : angle       0.99146 (    8)
  covalent geometry    : bond        0.00381 ( 6982)
  covalent geometry    : angle       0.81722 ( 9522)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 146
  time to evaluate  : 0.657 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 THR cc_start: 0.5170 (OUTLIER) cc_final: 0.4676 (p)
REVERT: A   74 ARG cc_start: 0.5704 (tmt170) cc_final: 0.5140 (ttp-170)
REVERT: A   83 SER cc_start: 0.7193 (t) cc_final: 0.6803 (p)
REVERT: A  182 PHE cc_start: 0.6732 (t80) cc_final: 0.6228 (t80)
REVERT: A  317 LEU cc_start: 0.6009 (OUTLIER) cc_final: 0.5475 (mt)
REVERT: B   73 THR cc_start: 0.5302 (OUTLIER) cc_final: 0.4816 (p)
REVERT: B   74 ARG cc_start: 0.5691 (tmt170) cc_final: 0.5144 (ttp-170)
REVERT: B   83 SER cc_start: 0.7106 (t) cc_final: 0.6744 (p)
REVERT: B  182 PHE cc_start: 0.6509 (OUTLIER) cc_final: 0.5833 (t80)
REVERT: B  317 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5489 (mt)
  outliers start: 32
  outliers final: 18
  residues processed: 162
  average time/residue: 0.1770
  time to fit residues: 38.0009
Evaluate side-chains
  159 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 136
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 PHE
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  465 TYR
Chi-restraints excluded: chain A residue  491 MET
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain B residue   50 PHE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  465 TYR
Chi-restraints excluded: chain B residue  491 MET
Chi-restraints excluded: chain B residue  539 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 14 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 48 optimal weight:    6.9990
   chunk 24 optimal weight:    0.3980
   chunk 70 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4976 r_free = 0.4976 target = 0.239930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4709 r_free = 0.4709 target = 0.211742 restraints weight = 11584.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4718 r_free = 0.4718 target = 0.213793 restraints weight = 8494.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4725 r_free = 0.4725 target = 0.215650 restraints weight = 6258.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.4748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6295
moved from start:          0.4421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6986  Z= 0.194
  Angle     :  0.861  11.458   9530  Z= 0.419
  Chirality :  0.047   0.301   1110
  Planarity :  0.005   0.055   1172
  Dihedral  :  5.057  35.706    940
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 17.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 24.50 %
    Favored  : 71.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.28), residues: 860
  helix:  1.01 (0.19), residues: 716
  sheet:  None (None), residues: 0
  loop : -3.55 (0.42), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  92 
 HIS   0.004   0.001   HIS B 525 
 PHE   0.030   0.002   PHE A  79 
 TYR   0.009   0.002   TYR A 337 
 ARG   0.003   0.000   ARG B 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04556 (  560)
  hydrogen bonds       : angle       4.76401 ( 1656)
  SS BOND              : bond        0.00513 (    4)
  SS BOND              : angle       1.38223 (    8)
  covalent geometry    : bond        0.00433 ( 6982)
  covalent geometry    : angle       0.86018 ( 9522)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 137
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 THR cc_start: 0.5473 (OUTLIER) cc_final: 0.4961 (p)
REVERT: A   74 ARG cc_start: 0.5784 (tmt170) cc_final: 0.5203 (ttp-170)
REVERT: A  201 TRP cc_start: 0.4277 (OUTLIER) cc_final: 0.3146 (m100)
REVERT: A  317 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.5771 (mt)
REVERT: B   73 THR cc_start: 0.5534 (OUTLIER) cc_final: 0.5021 (p)
REVERT: B   74 ARG cc_start: 0.5733 (tmt170) cc_final: 0.5165 (ttp-170)
REVERT: B   83 SER cc_start: 0.7165 (t) cc_final: 0.6810 (p)
REVERT: B  182 PHE cc_start: 0.6514 (OUTLIER) cc_final: 0.5758 (t80)
REVERT: B  317 LEU cc_start: 0.6377 (OUTLIER) cc_final: 0.5739 (mt)
  outliers start: 28
  outliers final: 21
  residues processed: 152
  average time/residue: 0.1849
  time to fit residues: 37.2253
Evaluate side-chains
  159 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 PHE
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  201 TRP
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  465 TYR
Chi-restraints excluded: chain A residue  491 MET
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain B residue   50 PHE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  254 LYS
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  465 TYR
Chi-restraints excluded: chain B residue  491 MET
Chi-restraints excluded: chain B residue  539 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 70 optimal weight:    0.8980
   chunk 63 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 78 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0980
   chunk 58 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 309 ASN
** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4982 r_free = 0.4982 target = 0.240539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4717 r_free = 0.4717 target = 0.212168 restraints weight = 11570.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4719 r_free = 0.4719 target = 0.213709 restraints weight = 8554.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4727 r_free = 0.4727 target = 0.214857 restraints weight = 7050.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.4748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6290
moved from start:          0.4545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6986  Z= 0.182
  Angle     :  0.878  11.972   9530  Z= 0.428
  Chirality :  0.049   0.297   1110
  Planarity :  0.005   0.063   1172
  Dihedral  :  5.077  30.642    940
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 17.27
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.09 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 25.21 %
    Favored  : 71.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.29), residues: 860
  helix:  1.06 (0.19), residues: 712
  sheet:  None (None), residues: 0
  loop : -3.58 (0.41), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  92 
 HIS   0.002   0.000   HIS B 525 
 PHE   0.020   0.001   PHE B 198 
 TYR   0.008   0.001   TYR A 337 
 ARG   0.005   0.000   ARG B 537 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04494 (  560)
  hydrogen bonds       : angle       4.73648 ( 1656)
  SS BOND              : bond        0.00012 (    4)
  SS BOND              : angle       3.58064 (    8)
  covalent geometry    : bond        0.00401 ( 6982)
  covalent geometry    : angle       0.87219 ( 9522)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 136
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 THR cc_start: 0.5494 (OUTLIER) cc_final: 0.4993 (p)
REVERT: A   74 ARG cc_start: 0.5770 (tmt170) cc_final: 0.5183 (ttp-170)
REVERT: A   85 LEU cc_start: 0.7041 (mm) cc_final: 0.6808 (tt)
REVERT: A  182 PHE cc_start: 0.6685 (t80) cc_final: 0.5952 (t80)
REVERT: A  201 TRP cc_start: 0.4260 (OUTLIER) cc_final: 0.3314 (m100)
REVERT: A  317 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.5747 (mt)
REVERT: A  526 CYS cc_start: 0.4303 (t) cc_final: 0.3982 (t)
REVERT: B   73 THR cc_start: 0.5574 (OUTLIER) cc_final: 0.5056 (p)
REVERT: B   74 ARG cc_start: 0.5719 (tmt170) cc_final: 0.5155 (ttp-170)
REVERT: B   83 SER cc_start: 0.6999 (t) cc_final: 0.6540 (p)
REVERT: B  182 PHE cc_start: 0.6746 (OUTLIER) cc_final: 0.5796 (t80)
REVERT: B  317 LEU cc_start: 0.6301 (OUTLIER) cc_final: 0.5641 (mt)
REVERT: B  320 MET cc_start: 0.7314 (mpp) cc_final: 0.6698 (mtm)
  outliers start: 26
  outliers final: 19
  residues processed: 151
  average time/residue: 0.1894
  time to fit residues: 37.7593
Evaluate side-chains
  157 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 PHE
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  201 TRP
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  465 TYR
Chi-restraints excluded: chain A residue  491 MET
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain B residue   50 PHE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  465 TYR
Chi-restraints excluded: chain B residue  491 MET
Chi-restraints excluded: chain B residue  539 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 62 optimal weight:    0.1980
   chunk 6 optimal weight:    3.9990
   chunk 59 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 309 ASN
** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 ASN
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4978 r_free = 0.4978 target = 0.240266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4685 r_free = 0.4685 target = 0.210072 restraints weight = 11812.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4730 r_free = 0.4730 target = 0.214774 restraints weight = 7273.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4757 r_free = 0.4757 target = 0.217515 restraints weight = 5358.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.4779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6224
moved from start:          0.4678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6986  Z= 0.188
  Angle     :  0.882  10.084   9530  Z= 0.434
  Chirality :  0.049   0.320   1110
  Planarity :  0.005   0.052   1172
  Dihedral  :  5.122  33.765    940
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 17.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 25.50 %
    Favored  : 70.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.29), residues: 860
  helix:  1.02 (0.19), residues: 718
  sheet:  None (None), residues: 0
  loop : -3.42 (0.44), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  92 
 HIS   0.002   0.000   HIS B 525 
 PHE   0.021   0.002   PHE A 198 
 TYR   0.008   0.001   TYR A 337 
 ARG   0.003   0.000   ARG B 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04587 (  560)
  hydrogen bonds       : angle       4.71788 ( 1656)
  SS BOND              : bond        0.00134 (    4)
  SS BOND              : angle       2.85431 (    8)
  covalent geometry    : bond        0.00416 ( 6982)
  covalent geometry    : angle       0.87844 ( 9522)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 THR cc_start: 0.5515 (OUTLIER) cc_final: 0.4991 (p)
REVERT: A   74 ARG cc_start: 0.5802 (tmt170) cc_final: 0.5200 (ttp-170)
REVERT: A   85 LEU cc_start: 0.7042 (mm) cc_final: 0.6766 (tt)
REVERT: A  182 PHE cc_start: 0.6768 (t80) cc_final: 0.6054 (t80)
REVERT: A  201 TRP cc_start: 0.4192 (OUTLIER) cc_final: 0.3209 (m100)
REVERT: A  317 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.5574 (mt)
REVERT: A  320 MET cc_start: 0.7334 (mpp) cc_final: 0.6758 (mtm)
REVERT: A  526 CYS cc_start: 0.4089 (t) cc_final: 0.3798 (t)
REVERT: B   73 THR cc_start: 0.5637 (OUTLIER) cc_final: 0.5120 (p)
REVERT: B   74 ARG cc_start: 0.5776 (tmt170) cc_final: 0.5192 (ttp-170)
REVERT: B   83 SER cc_start: 0.7059 (t) cc_final: 0.6634 (p)
REVERT: B  182 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6106 (t80)
REVERT: B  317 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.5620 (mt)
  outliers start: 26
  outliers final: 18
  residues processed: 149
  average time/residue: 0.1851
  time to fit residues: 36.7548
Evaluate side-chains
  157 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 PHE
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  201 TRP
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  465 TYR
Chi-restraints excluded: chain A residue  491 MET
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain B residue   50 PHE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  465 TYR
Chi-restraints excluded: chain B residue  491 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    8.9990
   chunk 49 optimal weight:    2.9990
   chunk 24 optimal weight:    0.3980
   chunk 71 optimal weight:    0.5980
   chunk 20 optimal weight:    0.2980
   chunk 76 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 80 optimal weight:    8.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 343 HIS
** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4979 r_free = 0.4979 target = 0.240384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.210237 restraints weight = 11787.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4729 r_free = 0.4729 target = 0.214747 restraints weight = 7298.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4758 r_free = 0.4758 target = 0.217641 restraints weight = 5398.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.4778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6221
moved from start:          0.4817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6986  Z= 0.183
  Angle     :  0.874   9.736   9530  Z= 0.429
  Chirality :  0.049   0.290   1110
  Planarity :  0.005   0.043   1172
  Dihedral  :  5.054  29.058    940
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 16.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 25.36 %
    Favored  : 70.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.29), residues: 860
  helix:  1.07 (0.19), residues: 718
  sheet:  None (None), residues: 0
  loop : -3.31 (0.45), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  67 
 HIS   0.001   0.000   HIS B 437 
 PHE   0.021   0.002   PHE B 198 
 TYR   0.008   0.001   TYR A 111 
 ARG   0.004   0.000   ARG B 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04513 (  560)
  hydrogen bonds       : angle       4.70095 ( 1656)
  SS BOND              : bond        0.00521 (    4)
  SS BOND              : angle       2.93655 (    8)
  covalent geometry    : bond        0.00407 ( 6982)
  covalent geometry    : angle       0.86987 ( 9522)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2548.13 seconds
wall clock time: 44 minutes 42.96 seconds (2682.96 seconds total)