Starting phenix.real_space_refine
on Fri Aug 22 18:24:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zat_39888/08_2025/8zat_39888.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zat_39888/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zat_39888/08_2025/8zat_39888.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zat_39888/08_2025/8zat_39888.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zat_39888/08_2025/8zat_39888.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zat_39888/08_2025/8zat_39888.map"
  }
  resolution = 3.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'ARG:plan': 1, 'PHE:plan': 2, 'GLU: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: {'ASP:plan': 1, 'ARG:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 24
  Time building chain proxies: 1.79, per 1000 atoms: 0.26
  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: 0.49
  Conformation dependent library (CDL) restraints added in 378.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.19
  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: 0.97

  Time building geometry restraints manager: 0.68 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: 0.01
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:             2.860
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.780
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.070
-------------------------------------------------------------------------------
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 : 12.17
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG B 432 
 TYR   0.010   0.001   TYR B  59 
 PHE   0.008   0.001   PHE B  65 
 TRP   0.006   0.001   TRP B  67 
 HIS   0.001   0.000   HIS A 434 

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

*********************** 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  : 0.254 
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: 0.6557 (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: 0.0878
  time to fit residues: 25.9411
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  : 0.265 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.1980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.2980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.5041 r_free = 0.5041 target = 0.248089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4798 r_free = 0.4798 target = 0.221874 restraints weight = 11881.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4788 r_free = 0.4788 target = 0.222431 restraints weight = 8107.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4794 r_free = 0.4794 target = 0.223040 restraints weight = 7194.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4801 r_free = 0.4801 target = 0.224415 restraints weight = 6120.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4802 r_free = 0.4802 target = 0.224495 restraints weight = 5888.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.4824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6126
moved from start:          0.2598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6986  Z= 0.178
  Angle     :  0.791   9.047   9530  Z= 0.383
  Chirality :  0.045   0.223   1110
  Planarity :  0.006   0.066   1172
  Dihedral  :  5.498  45.171    946
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 17.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.65 %
    Favored  : 75.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.30), residues: 860
  helix:  1.42 (0.20), residues: 724
  sheet:  None (None), residues: 0
  loop : -3.02 (0.49), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 432 
 TYR   0.016   0.002   TYR A 484 
 PHE   0.020   0.002   PHE B 416 
 TRP   0.011   0.001   TRP B  92 
 HIS   0.003   0.001   HIS B 525 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 6982)
  covalent geometry    : angle       0.79057 ( 9522)
  SS BOND              : bond        0.00545 (    4)
  SS BOND              : angle       0.98755 (    8)
  hydrogen bonds       : bond        0.04515 (  560)
  hydrogen bonds       : angle       4.69167 ( 1656)

*********************** 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
  180 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 157
  time to evaluate  : 0.238 
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   73 THR cc_start: 0.5102 (OUTLIER) cc_final: 0.4711 (p)
REVERT: A   74 ARG cc_start: 0.5597 (tmt170) cc_final: 0.4701 (tmm160)
REVERT: A   83 SER cc_start: 0.7274 (t) cc_final: 0.6927 (p)
REVERT: A  317 LEU cc_start: 0.5813 (OUTLIER) cc_final: 0.5301 (mt)
REVERT: A  333 MET cc_start: 0.5646 (mtp) cc_final: 0.4757 (ttm)
REVERT: B   73 THR cc_start: 0.5166 (OUTLIER) cc_final: 0.4755 (p)
REVERT: B   74 ARG cc_start: 0.5641 (tmt170) cc_final: 0.4748 (tmm160)
REVERT: B   83 SER cc_start: 0.7247 (t) cc_final: 0.6923 (p)
REVERT: B  317 LEU cc_start: 0.5765 (OUTLIER) cc_final: 0.5101 (mt)
REVERT: B  333 MET cc_start: 0.5663 (mtp) cc_final: 0.4754 (ttm)
  outliers start: 23
  outliers final: 6
  residues processed: 167
  average time/residue: 0.0810
  time to fit residues: 17.9572
Evaluate side-chains
  150 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 83 optimal weight:    9.9990
   chunk 63 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 60 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 ASN
** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.5015 r_free = 0.5015 target = 0.244889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4762 r_free = 0.4762 target = 0.217216 restraints weight = 11756.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4768 r_free = 0.4768 target = 0.219176 restraints weight = 7987.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4774 r_free = 0.4774 target = 0.220104 restraints weight = 6368.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4774 r_free = 0.4774 target = 0.220278 restraints weight = 5594.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4786 r_free = 0.4786 target = 0.222312 restraints weight = 5491.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.4811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6179
moved from start:          0.3087

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= 0.180
  Angle     :  0.776   8.521   9530  Z= 0.379
  Chirality :  0.046   0.278   1110
  Planarity :  0.005   0.062   1172
  Dihedral  :  4.975  36.392    940
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 17.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 22.36 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.30), residues: 860
  helix:  1.29 (0.20), residues: 734
  sheet:  None (None), residues: 0
  loop : -3.24 (0.53), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  29 
 TYR   0.019   0.002   TYR A 484 
 PHE   0.017   0.002   PHE B 416 
 TRP   0.009   0.001   TRP A  67 
 HIS   0.005   0.001   HIS A 525 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 6982)
  covalent geometry    : angle       0.77585 ( 9522)
  SS BOND              : bond        0.00319 (    4)
  SS BOND              : angle       0.56106 (    8)
  hydrogen bonds       : bond        0.04382 (  560)
  hydrogen bonds       : angle       4.63627 ( 1656)

*********************** 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
  180 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 147
  time to evaluate  : 0.265 
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: 0.5082 (OUTLIER) cc_final: 0.4661 (p)
REVERT: A   74 ARG cc_start: 0.5746 (tmt170) cc_final: 0.4810 (tmm160)
REVERT: A   83 SER cc_start: 0.7101 (t) cc_final: 0.6760 (p)
REVERT: A  317 LEU cc_start: 0.5669 (OUTLIER) cc_final: 0.5000 (mt)
REVERT: B   73 THR cc_start: 0.5210 (OUTLIER) cc_final: 0.4777 (p)
REVERT: B   74 ARG cc_start: 0.5729 (tmt170) cc_final: 0.4807 (tmm160)
REVERT: B   83 SER cc_start: 0.7083 (t) cc_final: 0.6727 (p)
REVERT: B  317 LEU cc_start: 0.5592 (OUTLIER) cc_final: 0.4768 (mt)
  outliers start: 33
  outliers final: 12
  residues processed: 160
  average time/residue: 0.0856
  time to fit residues: 18.2100
Evaluate side-chains
  151 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
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  317 LEU
Chi-restraints excluded: chain A residue  421 SER
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  317 LEU
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  421 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 86 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0970
   chunk 26 optimal weight:    2.9990
   chunk 10 optimal weight:    8.9990
   chunk 30 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0070
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.3996

-------------------------------------------------------------------------------
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 332 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 332 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 = 0.5025 r_free = 0.5025 target = 0.245554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4783 r_free = 0.4783 target = 0.219100 restraints weight = 11727.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4792 r_free = 0.4792 target = 0.221691 restraints weight = 8045.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4801 r_free = 0.4801 target = 0.223701 restraints weight = 5667.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4806 r_free = 0.4806 target = 0.224132 restraints weight = 5676.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4806 r_free = 0.4806 target = 0.224150 restraints weight = 4801.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.4834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6123
moved from start:          0.3345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6986  Z= 0.160
  Angle     :  0.765   8.724   9530  Z= 0.373
  Chirality :  0.045   0.246   1110
  Planarity :  0.005   0.060   1172
  Dihedral  :  5.025  38.227    940
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 15.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 24.22 %
    Favored  : 72.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.30), residues: 860
  helix:  1.30 (0.20), residues: 732
  sheet:  None (None), residues: 0
  loop : -3.30 (0.51), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  29 
 TYR   0.012   0.002   TYR B 484 
 PHE   0.012   0.001   PHE B 543 
 TRP   0.006   0.001   TRP A  92 
 HIS   0.005   0.001   HIS B 525 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6982)
  covalent geometry    : angle       0.76466 ( 9522)
  SS BOND              : bond        0.00394 (    4)
  SS BOND              : angle       0.90108 (    8)
  hydrogen bonds       : bond        0.04098 (  560)
  hydrogen bonds       : angle       4.56032 ( 1656)

*********************** 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: 21
    poor density    : 153
  time to evaluate  : 0.255 
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: 0.5140 (OUTLIER) cc_final: 0.4723 (p)
REVERT: A   74 ARG cc_start: 0.5798 (tmt170) cc_final: 0.4835 (tmm160)
REVERT: A   83 SER cc_start: 0.7022 (t) cc_final: 0.6709 (p)
REVERT: A  182 PHE cc_start: 0.6301 (t80) cc_final: 0.5865 (t80)
REVERT: A  317 LEU cc_start: 0.5529 (OUTLIER) cc_final: 0.4858 (mt)
REVERT: B   73 THR cc_start: 0.5150 (OUTLIER) cc_final: 0.4708 (p)
REVERT: B   74 ARG cc_start: 0.5750 (tmt170) cc_final: 0.4815 (tmm160)
REVERT: B   83 SER cc_start: 0.6999 (t) cc_final: 0.6697 (p)
REVERT: B  182 PHE cc_start: 0.6313 (t80) cc_final: 0.5861 (t80)
REVERT: B  317 LEU cc_start: 0.5441 (OUTLIER) cc_final: 0.4771 (mt)
  outliers start: 21
  outliers final: 10
  residues processed: 162
  average time/residue: 0.0724
  time to fit residues: 15.5752
Evaluate side-chains
  150 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 136
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
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   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 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  234 VAL
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  383 VAL
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 86 optimal weight:    0.9980
   chunk 39 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0770
   chunk 72 optimal weight:    0.0670
   chunk 27 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 56 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 3 optimal weight:    7.9990
   overall best weight:    0.5476

-------------------------------------------------------------------------------
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 332 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 332 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 = 0.5020 r_free = 0.5020 target = 0.244606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4762 r_free = 0.4762 target = 0.217678 restraints weight = 11795.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4771 r_free = 0.4771 target = 0.219736 restraints weight = 8105.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4772 r_free = 0.4772 target = 0.220337 restraints weight = 6043.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4776 r_free = 0.4776 target = 0.220936 restraints weight = 6137.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4778 r_free = 0.4778 target = 0.221216 restraints weight = 5537.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.4803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6182
moved from start:          0.3586

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= 0.168
  Angle     :  0.800   8.944   9530  Z= 0.391
  Chirality :  0.046   0.242   1110
  Planarity :  0.005   0.054   1172
  Dihedral  :  4.981  33.699    940
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 15.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 23.08 %
    Favored  : 72.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.29), residues: 860
  helix:  1.27 (0.20), residues: 720
  sheet:  None (None), residues: 0
  loop : -3.18 (0.45), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  29 
 TYR   0.027   0.002   TYR A 541 
 PHE   0.018   0.001   PHE A  79 
 TRP   0.005   0.001   TRP B  92 
 HIS   0.001   0.000   HIS B 525 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 6982)
  covalent geometry    : angle       0.79988 ( 9522)
  SS BOND              : bond        0.00255 (    4)
  SS BOND              : angle       0.45671 (    8)
  hydrogen bonds       : bond        0.04133 (  560)
  hydrogen bonds       : angle       4.60935 ( 1656)

*********************** 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
  178 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 144
  time to evaluate  : 0.273 
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: 0.5135 (OUTLIER) cc_final: 0.4702 (p)
REVERT: A   74 ARG cc_start: 0.5710 (tmt170) cc_final: 0.5177 (ttp-170)
REVERT: A   83 SER cc_start: 0.7032 (t) cc_final: 0.6697 (p)
REVERT: A  182 PHE cc_start: 0.6263 (t80) cc_final: 0.5826 (t80)
REVERT: A  317 LEU cc_start: 0.5607 (OUTLIER) cc_final: 0.4925 (mt)
REVERT: B   73 THR cc_start: 0.5109 (OUTLIER) cc_final: 0.4685 (p)
REVERT: B   74 ARG cc_start: 0.5790 (tmt170) cc_final: 0.5242 (ttp-170)
REVERT: B   83 SER cc_start: 0.6980 (t) cc_final: 0.6658 (p)
REVERT: B  182 PHE cc_start: 0.6330 (t80) cc_final: 0.5887 (t80)
REVERT: B  317 LEU cc_start: 0.5615 (OUTLIER) cc_final: 0.4928 (mt)
REVERT: B  333 MET cc_start: 0.6115 (ttm) cc_final: 0.4676 (ttm)
  outliers start: 34
  outliers final: 14
  residues processed: 162
  average time/residue: 0.0849
  time to fit residues: 18.2203
Evaluate side-chains
  158 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
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  383 VAL
Chi-restraints excluded: chain A residue  465 TYR
Chi-restraints excluded: chain A residue  491 MET
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  117 LEU
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  465 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 67 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 84 optimal weight:    6.9990
   chunk 14 optimal weight:    0.2980
   chunk 3 optimal weight:    0.1980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 334 GLN
** 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 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 464 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5014 r_free = 0.5014 target = 0.244177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4738 r_free = 0.4738 target = 0.216159 restraints weight = 11798.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4775 r_free = 0.4775 target = 0.220014 restraints weight = 7540.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4798 r_free = 0.4798 target = 0.222475 restraints weight = 5701.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4806 r_free = 0.4806 target = 0.223590 restraints weight = 4782.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4819 r_free = 0.4819 target = 0.224672 restraints weight = 4354.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.4840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6062
moved from start:          0.3828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6986  Z= 0.162
  Angle     :  0.795   9.653   9530  Z= 0.385
  Chirality :  0.046   0.236   1110
  Planarity :  0.005   0.055   1172
  Dihedral  :  5.010  36.953    940
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 23.93 %
    Favored  : 72.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.29), residues: 860
  helix:  1.30 (0.20), residues: 718
  sheet:  None (None), residues: 0
  loop : -3.37 (0.44), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  29 
 TYR   0.018   0.002   TYR A 541 
 PHE   0.023   0.001   PHE A  79 
 TRP   0.008   0.001   TRP B  67 
 HIS   0.002   0.000   HIS A 525 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6982)
  covalent geometry    : angle       0.79525 ( 9522)
  SS BOND              : bond        0.00044 (    4)
  SS BOND              : angle       0.49869 (    8)
  hydrogen bonds       : bond        0.04058 (  560)
  hydrogen bonds       : angle       4.58182 ( 1656)

*********************** 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
  178 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 153
  time to evaluate  : 0.205 
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: 0.5199 (OUTLIER) cc_final: 0.4733 (p)
REVERT: A   74 ARG cc_start: 0.5718 (tmt170) cc_final: 0.5191 (ttp-170)
REVERT: A   83 SER cc_start: 0.7055 (t) cc_final: 0.6751 (p)
REVERT: A  182 PHE cc_start: 0.6227 (t80) cc_final: 0.5759 (t80)
REVERT: A  317 LEU cc_start: 0.5678 (OUTLIER) cc_final: 0.5027 (mt)
REVERT: B   73 THR cc_start: 0.5315 (OUTLIER) cc_final: 0.4865 (p)
REVERT: B   74 ARG cc_start: 0.5825 (tmt170) cc_final: 0.5280 (ttp-170)
REVERT: B   83 SER cc_start: 0.7091 (t) cc_final: 0.6789 (p)
REVERT: B  182 PHE cc_start: 0.6204 (t80) cc_final: 0.5748 (t80)
REVERT: B  317 LEU cc_start: 0.5744 (OUTLIER) cc_final: 0.5064 (mt)
  outliers start: 25
  outliers final: 12
  residues processed: 164
  average time/residue: 0.0812
  time to fit residues: 17.5558
Evaluate side-chains
  160 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
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  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  234 VAL
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  465 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 1 optimal weight:    0.3980
   chunk 25 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 82 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   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 332 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 332 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 = 0.4998 r_free = 0.4998 target = 0.242432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4726 r_free = 0.4726 target = 0.214442 restraints weight = 11588.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4763 r_free = 0.4763 target = 0.218399 restraints weight = 7393.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4787 r_free = 0.4787 target = 0.220835 restraints weight = 5568.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4793 r_free = 0.4793 target = 0.221672 restraints weight = 4679.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4799 r_free = 0.4799 target = 0.222547 restraints weight = 4314.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.4824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6112
moved from start:          0.4039

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= 0.176
  Angle     :  0.827  13.595   9530  Z= 0.399
  Chirality :  0.047   0.233   1110
  Planarity :  0.005   0.049   1172
  Dihedral  :  4.968  31.211    940
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 16.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 23.93 %
    Favored  : 72.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.29), residues: 860
  helix:  1.23 (0.19), residues: 714
  sheet:  None (None), residues: 0
  loop : -3.40 (0.42), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  29 
 TYR   0.013   0.002   TYR A 541 
 PHE   0.027   0.002   PHE B  79 
 TRP   0.007   0.001   TRP B  67 
 HIS   0.004   0.001   HIS B 525 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 6982)
  covalent geometry    : angle       0.82728 ( 9522)
  SS BOND              : bond        0.00008 (    4)
  SS BOND              : angle       0.54352 (    8)
  hydrogen bonds       : bond        0.04219 (  560)
  hydrogen bonds       : angle       4.64340 ( 1656)

*********************** 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
  171 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 143
  time to evaluate  : 0.250 
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: 0.5189 (OUTLIER) cc_final: 0.4703 (p)
REVERT: A   74 ARG cc_start: 0.5752 (tmt170) cc_final: 0.5205 (ttp-170)
REVERT: A   83 SER cc_start: 0.7142 (t) cc_final: 0.6848 (p)
REVERT: A  182 PHE cc_start: 0.6234 (t80) cc_final: 0.5761 (t80)
REVERT: A  317 LEU cc_start: 0.5891 (OUTLIER) cc_final: 0.5222 (mt)
REVERT: B   73 THR cc_start: 0.5341 (OUTLIER) cc_final: 0.4858 (p)
REVERT: B   74 ARG cc_start: 0.5762 (tmt170) cc_final: 0.5216 (ttp-170)
REVERT: B   83 SER cc_start: 0.7121 (t) cc_final: 0.6828 (p)
REVERT: B  182 PHE cc_start: 0.6224 (t80) cc_final: 0.5754 (t80)
REVERT: B  317 LEU cc_start: 0.5927 (OUTLIER) cc_final: 0.5230 (mt)
  outliers start: 28
  outliers final: 17
  residues processed: 155
  average time/residue: 0.0789
  time to fit residues: 16.4529
Evaluate side-chains
  160 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
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  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  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  117 LEU
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  465 TYR
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 68 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 36 optimal weight:    8.9990
   chunk 20 optimal weight:    0.0030
   chunk 54 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    0.9192

-------------------------------------------------------------------------------
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 332 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 332 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 = 0.4980 r_free = 0.4980 target = 0.240291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4702 r_free = 0.4702 target = 0.211661 restraints weight = 11706.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4741 r_free = 0.4741 target = 0.215734 restraints weight = 7517.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4763 r_free = 0.4763 target = 0.218064 restraints weight = 5649.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4771 r_free = 0.4771 target = 0.219145 restraints weight = 4756.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.4784 r_free = 0.4784 target = 0.220259 restraints weight = 4339.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.4802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6176
moved from start:          0.4350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6986  Z= 0.201
  Angle     :  0.862  12.731   9530  Z= 0.421
  Chirality :  0.048   0.238   1110
  Planarity :  0.005   0.053   1172
  Dihedral  :  5.054  36.054    940
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 16.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 25.36 %
    Favored  : 71.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.29), residues: 860
  helix:  1.02 (0.19), residues: 730
  sheet:  None (None), residues: 0
  loop : -3.70 (0.44), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 100 
 TYR   0.011   0.002   TYR A 541 
 PHE   0.031   0.002   PHE B  79 
 TRP   0.007   0.001   TRP B  67 
 HIS   0.006   0.001   HIS A 525 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 6982)
  covalent geometry    : angle       0.86185 ( 9522)
  SS BOND              : bond        0.00492 (    4)
  SS BOND              : angle       1.16629 (    8)
  hydrogen bonds       : bond        0.04512 (  560)
  hydrogen bonds       : angle       4.78519 ( 1656)

*********************** 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
  164 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 THR cc_start: 0.5475 (OUTLIER) cc_final: 0.4970 (p)
REVERT: A   74 ARG cc_start: 0.5839 (tmt170) cc_final: 0.5258 (ttp-170)
REVERT: A  182 PHE cc_start: 0.6294 (t80) cc_final: 0.5831 (t80)
REVERT: A  317 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5641 (mt)
REVERT: B   73 THR cc_start: 0.5607 (OUTLIER) cc_final: 0.5077 (p)
REVERT: B   74 ARG cc_start: 0.5762 (tmt170) cc_final: 0.5197 (ttp-170)
REVERT: B   83 SER cc_start: 0.7229 (t) cc_final: 0.6876 (p)
REVERT: B  182 PHE cc_start: 0.6268 (t80) cc_final: 0.5816 (t80)
REVERT: B  317 LEU cc_start: 0.6178 (OUTLIER) cc_final: 0.5554 (mt)
REVERT: B  526 CYS cc_start: 0.3925 (t) cc_final: 0.3672 (t)
  outliers start: 24
  outliers final: 15
  residues processed: 151
  average time/residue: 0.0741
  time to fit residues: 14.9011
Evaluate side-chains
  153 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
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  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  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  117 LEU
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  465 TYR
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 43 optimal weight:    0.4980
   chunk 25 optimal weight:    9.9990
   chunk 79 optimal weight:    0.3980
   chunk 64 optimal weight:    0.2980
   chunk 49 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 55 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9990
   chunk 69 optimal weight:    9.9990
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 332 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 332 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 = 0.4992 r_free = 0.4992 target = 0.241299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4707 r_free = 0.4707 target = 0.212250 restraints weight = 11709.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4743 r_free = 0.4743 target = 0.216151 restraints weight = 7654.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4766 r_free = 0.4766 target = 0.218645 restraints weight = 5865.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4775 r_free = 0.4775 target = 0.219834 restraints weight = 4956.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4787 r_free = 0.4787 target = 0.220859 restraints weight = 4516.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.4813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6127
moved from start:          0.4473

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= 0.179
  Angle     :  0.889  14.766   9530  Z= 0.425
  Chirality :  0.049   0.338   1110
  Planarity :  0.006   0.083   1172
  Dihedral  :  5.029  31.071    940
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 16.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 25.78 %
    Favored  : 70.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.29), residues: 860
  helix:  1.09 (0.19), residues: 714
  sheet:  None (None), residues: 0
  loop : -3.39 (0.43), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 432 
 TYR   0.011   0.001   TYR B 541 
 PHE   0.017   0.001   PHE A 499 
 TRP   0.007   0.001   TRP B  67 
 HIS   0.007   0.001   HIS A 525 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 6982)
  covalent geometry    : angle       0.88759 ( 9522)
  SS BOND              : bond        0.00335 (    4)
  SS BOND              : angle       1.84777 (    8)
  hydrogen bonds       : bond        0.04371 (  560)
  hydrogen bonds       : angle       4.79763 ( 1656)

*********************** 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: 23
    poor density    : 139
  time to evaluate  : 0.260 
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: 0.5506 (OUTLIER) cc_final: 0.4989 (p)
REVERT: A   74 ARG cc_start: 0.5796 (tmt170) cc_final: 0.5228 (ttp-170)
REVERT: A   83 SER cc_start: 0.7178 (t) cc_final: 0.6828 (p)
REVERT: A   85 LEU cc_start: 0.6977 (mm) cc_final: 0.6760 (tt)
REVERT: A  317 LEU cc_start: 0.6058 (OUTLIER) cc_final: 0.5571 (mt)
REVERT: B   73 THR cc_start: 0.5632 (OUTLIER) cc_final: 0.5097 (p)
REVERT: B   74 ARG cc_start: 0.5816 (tmt170) cc_final: 0.5242 (ttp-170)
REVERT: B   83 SER cc_start: 0.7170 (t) cc_final: 0.6815 (p)
REVERT: B   85 LEU cc_start: 0.6978 (mm) cc_final: 0.6732 (tt)
REVERT: B  317 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5514 (mt)
REVERT: B  526 CYS cc_start: 0.4058 (t) cc_final: 0.3797 (t)
  outliers start: 23
  outliers final: 15
  residues processed: 151
  average time/residue: 0.0820
  time to fit residues: 16.5862
Evaluate side-chains
  151 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
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  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  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  117 LEU
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  465 TYR
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 17 optimal weight:    0.6980
   chunk 50 optimal weight:    5.9990
   chunk 59 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 53 optimal weight:    0.3980
   chunk 28 optimal weight:    0.1980
   chunk 82 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 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 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 332 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 = 0.4993 r_free = 0.4993 target = 0.241413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4736 r_free = 0.4736 target = 0.213661 restraints weight = 11657.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4739 r_free = 0.4739 target = 0.215185 restraints weight = 8432.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4745 r_free = 0.4745 target = 0.215999 restraints weight = 6866.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4753 r_free = 0.4753 target = 0.217752 restraints weight = 6005.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4754 r_free = 0.4754 target = 0.217891 restraints weight = 5967.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.4776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6218
moved from start:          0.4622

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= 0.182
  Angle     :  0.921  13.797   9530  Z= 0.444
  Chirality :  0.050   0.342   1110
  Planarity :  0.005   0.051   1172
  Dihedral  :  5.165  33.577    940
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 16.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 25.50 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.29), residues: 860
  helix:  1.12 (0.19), residues: 716
  sheet:  None (None), residues: 0
  loop : -3.45 (0.43), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 100 
 TYR   0.044   0.002   TYR B 337 
 PHE   0.021   0.001   PHE B 198 
 TRP   0.012   0.001   TRP B  67 
 HIS   0.003   0.000   HIS A 525 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 6982)
  covalent geometry    : angle       0.91196 ( 9522)
  SS BOND              : bond        0.00462 (    4)
  SS BOND              : angle       4.43739 (    8)
  hydrogen bonds       : bond        0.04450 (  560)
  hydrogen bonds       : angle       4.71144 ( 1656)

********************** 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: 21
    poor density    : 140
  time to evaluate  : 0.286 
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: 0.5500 (OUTLIER) cc_final: 0.4980 (p)
REVERT: A   74 ARG cc_start: 0.5766 (tmt170) cc_final: 0.5188 (ttp-170)
REVERT: A   83 SER cc_start: 0.6887 (t) cc_final: 0.6557 (p)
REVERT: A   85 LEU cc_start: 0.7004 (mm) cc_final: 0.6759 (tt)
REVERT: A  182 PHE cc_start: 0.6586 (t80) cc_final: 0.6022 (t80)
REVERT: A  317 LEU cc_start: 0.6184 (OUTLIER) cc_final: 0.5590 (mt)
REVERT: B   73 THR cc_start: 0.5629 (OUTLIER) cc_final: 0.5077 (p)
REVERT: B   74 ARG cc_start: 0.5795 (tmt170) cc_final: 0.5222 (ttp-170)
REVERT: B   83 SER cc_start: 0.6946 (t) cc_final: 0.6528 (p)
REVERT: B  182 PHE cc_start: 0.6647 (t80) cc_final: 0.5947 (t80)
REVERT: B  317 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.5732 (mt)
REVERT: B  320 MET cc_start: 0.7441 (mpp) cc_final: 0.6824 (mtm)
REVERT: B  526 CYS cc_start: 0.4421 (t) cc_final: 0.4137 (t)
  outliers start: 21
  outliers final: 15
  residues processed: 152
  average time/residue: 0.0844
  time to fit residues: 16.9819
Evaluate side-chains
  156 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
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  117 LEU
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 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  117 LEU
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  465 TYR
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 62 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 63 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 79 optimal weight:    0.0970
   chunk 26 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 7 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.5178

-------------------------------------------------------------------------------
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
** A 332 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 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 = 0.4993 r_free = 0.4993 target = 0.241379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4747 r_free = 0.4747 target = 0.214397 restraints weight = 11664.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4751 r_free = 0.4751 target = 0.215847 restraints weight = 8426.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4758 r_free = 0.4758 target = 0.216792 restraints weight = 6679.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4758 r_free = 0.4758 target = 0.216913 restraints weight = 5881.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4769 r_free = 0.4769 target = 0.218838 restraints weight = 5808.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.4796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6192
moved from start:          0.4756

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= 0.180
  Angle     :  0.915  16.745   9530  Z= 0.439
  Chirality :  0.050   0.331   1110
  Planarity :  0.005   0.044   1172
  Dihedral  :  5.135  29.511    940
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 17.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 25.50 %
    Favored  : 71.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.29), residues: 860
  helix:  1.18 (0.20), residues: 714
  sheet:  None (None), residues: 0
  loop : -3.43 (0.43), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 537 
 TYR   0.014   0.002   TYR B 435 
 PHE   0.026   0.001   PHE B  79 
 TRP   0.011   0.001   TRP B  67 
 HIS   0.002   0.000   HIS B 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 6982)
  covalent geometry    : angle       0.90952 ( 9522)
  SS BOND              : bond        0.00122 (    4)
  SS BOND              : angle       3.41656 (    8)
  hydrogen bonds       : bond        0.04380 (  560)
  hydrogen bonds       : angle       4.70393 ( 1656)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1263.57 seconds
wall clock time: 22 minutes 25.49 seconds (1345.49 seconds total)