Starting phenix.real_space_refine
on Tue Jan 14 06:07:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ur7_42486/01_2025/8ur7_42486.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ur7_42486/01_2025/8ur7_42486.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ur7_42486/01_2025/8ur7_42486.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ur7_42486/01_2025/8ur7_42486.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ur7_42486/01_2025/8ur7_42486.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ur7_42486/01_2025/8ur7_42486.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.115
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      18      5.16       5
     C    3795      2.51       5
     N     999      2.21       5
     O     960      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 5772
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1882
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 1882
          Classifications: {'peptide': 263}
          Incomplete info: {'truncation_to_alanine': 83}
          Link IDs: {'PTRANS': 14, 'TRANS': 248}
          Unresolved non-hydrogen bonds: 240
          Unresolved non-hydrogen angles: 294
          Unresolved non-hydrogen dihedrals: 186
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 21, 'ASN:plan1': 9, 'ARG:plan': 4, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 154
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 3.33, per 1000 atoms: 0.58
  Number of scatterers: 5772
  At special positions: 0
  Unit cell: (82.8298, 85.686, 119.96, 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      18     16.00
     O     960      8.00
     N     999      7.00
     C    3795      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  59 " - pdb=" SG  CYS A  71 " distance=2.10
    Simple disulfide: pdb=" SG  CYS A  94 " - pdb=" SG  CYS A 139 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 107 " - pdb=" SG  CYS A 271 " distance=2.18

  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
  Links applied
    NAG-ASN
      " NAG A 501 " - " ASN A  58 "
      " NAG A 502 " - " ASN A 163 "
      " NAG A 503 " - " ASN A 129 "
      " NAG B 501 " - " ASN B  58 "
      " NAG B 502 " - " ASN B 163 "
      " NAG B 503 " - " ASN B 129 "
      " NAG C 501 " - " ASN C  58 "
      " NAG C 502 " - " ASN C 163 "
      " NAG C 503 " - " ASN C 129 "
  Time building additional restraints: 1.26
  Conformation dependent library (CDL) restraints added in 779.4 milliseconds
  

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1470

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 12 sheets defined
      27.0% alpha, 27.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 60 through 67
    Processing helix  chain 'A' and resid 101 through 109
    Processing helix  chain 'A' and resid 187 through 196
    Processing helix  chain 'A' and resid 270 through 313
    Processing helix  chain 'B' and resid 60 through 67
    Processing helix  chain 'B' and resid 101 through 109
    Processing helix  chain 'B' and resid 187 through 196
    Processing helix  chain 'B' and resid 270 through 313
    Processing helix  chain 'C' and resid 60 through 67
    Processing helix  chain 'C' and resid 101 through 109
    Processing helix  chain 'C' and resid 187 through 196
    Processing helix  chain 'C' and resid 270 through 313
    Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 119
      removed outlier: 6.478A  pdb=" N   TYR A 256 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 4.961A  pdb=" N   LEU A 179 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   LEU A 179 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 119
      removed outlier: 6.478A  pdb=" N   TYR A 256 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 4.961A  pdb=" N   LEU A 179 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 141
      removed outlier: 4.469A  pdb=" N   CYS A 139 " --> pdb=" O   SER A 146 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   SER A 146 " --> pdb=" O   CYS A 139 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 164 through 169
    Processing sheet with id=AA5, first strand: chain 'B' and resid 115 through 119
      removed outlier: 6.478A  pdb=" N   TYR B 256 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   LEU B 179 " --> pdb=" O   TYR B 256 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   LEU B 179 " --> pdb=" O   PRO B 254 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 115 through 119
      removed outlier: 6.478A  pdb=" N   TYR B 256 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   LEU B 179 " --> pdb=" O   TYR B 256 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 136 through 141
      removed outlier: 4.470A  pdb=" N   CYS B 139 " --> pdb=" O   SER B 146 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   SER B 146 " --> pdb=" O   CYS B 139 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 169
    Processing sheet with id=AA9, first strand: chain 'C' and resid 115 through 119
      removed outlier: 6.479A  pdb=" N   TYR C 256 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
      removed outlier: 4.961A  pdb=" N   LEU C 179 " --> pdb=" O   TYR C 256 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   LEU C 179 " --> pdb=" O   PRO C 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 115 through 119
      removed outlier: 6.479A  pdb=" N   TYR C 256 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
      removed outlier: 4.961A  pdb=" N   LEU C 179 " --> pdb=" O   TYR C 256 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 141
      removed outlier: 4.470A  pdb=" N   CYS C 139 " --> pdb=" O   SER C 146 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   SER C 146 " --> pdb=" O   CYS C 139 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 164 through 169

    309 hydrogen bonds defined for protein.
    864 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.57

  Time building geometry restraints manager: 1.50 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1182
        1.33 -     1.45: 1482
        1.45 -     1.57: 3267
        1.57 -     1.69: 3
        1.69 -     1.81: 18
  Bond restraints: 5952
  Sorted by residual:
  bond pdb=" C   ALA C  52 "
       pdb=" N   PRO C  53 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 9.40e-03 1.13e+04 7.48e+00
  bond pdb=" C5  NAG A 501 "
       pdb=" O5  NAG A 501 "
    ideal  model  delta    sigma   weight residual
    1.413  1.467 -0.054 2.00e-02 2.50e+03 7.33e+00
  bond pdb=" C5  NAG C 501 "
       pdb=" O5  NAG C 501 "
    ideal  model  delta    sigma   weight residual
    1.413  1.467 -0.054 2.00e-02 2.50e+03 7.29e+00
  bond pdb=" C   ALA A  52 "
       pdb=" N   PRO A  53 "
    ideal  model  delta    sigma   weight residual
    1.335  1.360 -0.025 9.40e-03 1.13e+04 7.28e+00
  bond pdb=" C5  NAG B 501 "
       pdb=" O5  NAG B 501 "
    ideal  model  delta    sigma   weight residual
    1.413  1.467 -0.054 2.00e-02 2.50e+03 7.28e+00
  ... (remaining 5947 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 6974
        1.63 -     3.25: 1014
        3.25 -     4.88: 106
        4.88 -     6.50: 66
        6.50 -     8.13: 27
  Bond angle restraints: 8187
  Sorted by residual:
  angle pdb=" C   HIS A 184 "
        pdb=" N   PRO A 185 "
        pdb=" CA  PRO A 185 "
      ideal   model   delta    sigma   weight residual
     119.66  126.50   -6.84 7.30e-01 1.88e+00 8.79e+01
  angle pdb=" C   HIS B 184 "
        pdb=" N   PRO B 185 "
        pdb=" CA  PRO B 185 "
      ideal   model   delta    sigma   weight residual
     119.66  126.48   -6.82 7.30e-01 1.88e+00 8.73e+01
  angle pdb=" C   HIS C 184 "
        pdb=" N   PRO C 185 "
        pdb=" CA  PRO C 185 "
      ideal   model   delta    sigma   weight residual
     119.66  126.44   -6.78 7.30e-01 1.88e+00 8.63e+01
  angle pdb=" C   ASN B  88 "
        pdb=" N   PRO B  89 "
        pdb=" CA  PRO B  89 "
      ideal   model   delta    sigma   weight residual
     120.31  127.70   -7.39 9.80e-01 1.04e+00 5.69e+01
  angle pdb=" C   ASN A  88 "
        pdb=" N   PRO A  89 "
        pdb=" CA  PRO A  89 "
      ideal   model   delta    sigma   weight residual
     120.31  127.67   -7.36 9.80e-01 1.04e+00 5.63e+01
  ... (remaining 8182 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 3386
       17.27 -    34.53: 85
       34.53 -    51.80: 14
       51.80 -    69.07: 0
       69.07 -    86.33: 7
  Dihedral angle restraints: 3492
    sinusoidal: 1194
      harmonic: 2298
  Sorted by residual:
  dihedral pdb=" CB  CYS A  94 "
           pdb=" SG  CYS A  94 "
           pdb=" SG  CYS A 139 "
           pdb=" CB  CYS A 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.10  -80.10     1      1.00e+01 1.00e-02 7.95e+01
  dihedral pdb=" CB  CYS A  59 "
           pdb=" SG  CYS A  59 "
           pdb=" SG  CYS A  71 "
           pdb=" CB  CYS A  71 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -121.36   35.36     1      1.00e+01 1.00e-02 1.77e+01
  dihedral pdb=" CB  GLU C 119 "
           pdb=" CG  GLU C 119 "
           pdb=" CD  GLU C 119 "
           pdb=" OE1 GLU C 119 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -72.13   72.13     1      3.00e+01 1.11e-03 7.39e+00
  ... (remaining 3489 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 659
       0.065 -    0.130: 210
       0.130 -    0.194: 52
       0.194 -    0.259: 18
       0.259 -    0.324: 9
  Chirality restraints: 948
  Sorted by residual:
  chirality pdb=" C2  NAG C 502 "
            pdb=" C1  NAG C 502 "
            pdb=" C3  NAG C 502 "
            pdb=" N2  NAG C 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.82    0.32 2.00e-01 2.50e+01 2.63e+00
  chirality pdb=" C2  NAG B 502 "
            pdb=" C1  NAG B 502 "
            pdb=" C3  NAG B 502 "
            pdb=" N2  NAG B 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.81    0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" C2  NAG A 502 "
            pdb=" C1  NAG A 502 "
            pdb=" C3  NAG A 502 "
            pdb=" N2  NAG A 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.81    0.32 2.00e-01 2.50e+01 2.55e+00
  ... (remaining 945 not shown)

  Planarity restraints: 1041
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 232 "    0.025 2.00e-02 2.50e+03   1.36e-02 3.72e+00
        pdb=" CG  TYR C 232 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 232 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 232 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 232 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 232 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 232 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C 232 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 232 "    0.025 2.00e-02 2.50e+03   1.36e-02 3.71e+00
        pdb=" CG  TYR B 232 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 232 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 232 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 232 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 232 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 232 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 232 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 232 "    0.025 2.00e-02 2.50e+03   1.36e-02 3.68e+00
        pdb=" CG  TYR A 232 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 232 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 232 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 232 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 232 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 232 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 232 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1038 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 27
        2.60 -     3.17: 4771
        3.17 -     3.75: 8569
        3.75 -     4.32: 11917
        4.32 -     4.90: 18900
  Nonbonded interactions: 44184
  Sorted by model distance:
  nonbonded pdb=" SG  CYS B  94 "
            pdb=" SG  CYS B 139 "
     model   vdw
     2.021 3.760
  nonbonded pdb=" SG  CYS C  94 "
            pdb=" SG  CYS C 139 "
     model   vdw
     2.022 3.760
  nonbonded pdb=" SG  CYS B  59 "
            pdb=" SG  CYS B  71 "
     model   vdw
     2.096 3.760
  nonbonded pdb=" SG  CYS C  59 "
            pdb=" SG  CYS C  71 "
     model   vdw
     2.097 3.760
  nonbonded pdb=" SG  CYS B 107 "
            pdb=" SG  CYS B 271 "
     model   vdw
     2.181 3.760
  ... (remaining 44179 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  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:             0.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.230
  Find NCS groups from input model:        0.110
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7154
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      :  0.009   0.054   5952  Z= 0.636
  Angle     :  1.277   8.129   8187  Z= 0.892
  Chirality :  0.075   0.324    948
  Planarity :  0.005   0.018   1032
  Dihedral  :  9.351  86.333   2013
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  3.31 %
    Favored  : 96.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.27), residues: 783
  helix:  0.32 (0.34), residues: 201
  sheet:  1.20 (0.31), residues: 198
  loop : -1.30 (0.28), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP C  80 
 HIS   0.003   0.001   HIS A 130 
 PHE   0.013   0.003   PHE B 115 
 TYR   0.025   0.005   TYR B 232 
 ARG   0.002   0.000   ARG C 117 

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 158
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  102 TYR cc_start: 0.9012 (t80) cc_final: 0.8386 (t80)
REVERT: B  172 LYS cc_start: 0.8808 (mmtt) cc_final: 0.8595 (mmtt)
REVERT: B  223 VAL cc_start: 0.9057 (t) cc_final: 0.8570 (p)
REVERT: B  229 ARG cc_start: 0.8526 (mmt-90) cc_final: 0.8225 (mmt90)
REVERT: B  295 HIS cc_start: 0.8473 (t70) cc_final: 0.7975 (t-170)
REVERT: C  102 TYR cc_start: 0.9060 (t80) cc_final: 0.8738 (t80)
REVERT: C  147 PHE cc_start: 0.6582 (t80) cc_final: 0.6143 (t80)
REVERT: C  172 LYS cc_start: 0.8734 (mmtt) cc_final: 0.8519 (mmmt)
  outliers start: 3
  outliers final: 0
  residues processed: 161
  average time/residue: 0.2315
  time to fit residues: 45.7789
Evaluate side-chains
  92 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 37 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 130 HIS
B 108 GLN
C 130 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.183568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.148564 restraints weight = 8082.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.151021 restraints weight = 6121.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.153163 restraints weight = 5061.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5952  Z= 0.260
  Angle     :  0.632   6.804   8187  Z= 0.339
  Chirality :  0.046   0.169    948
  Planarity :  0.004   0.027   1032
  Dihedral  :  7.346  97.381   1038
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 14.35 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.28), residues: 783
  helix:  1.60 (0.36), residues: 210
  sheet:  1.17 (0.32), residues: 204
  loop : -1.19 (0.29), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 153 
 HIS   0.004   0.001   HIS A 183 
 PHE   0.029   0.002   PHE A 115 
 TYR   0.014   0.002   TYR C 195 
 ARG   0.006   0.001   ARG C 305 

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
  outliers start: 12
  outliers final: 11
  residues processed: 114
  average time/residue: 0.2011
  time to fit residues: 29.0099
Evaluate side-chains
  101 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  302 HIS
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  307 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 17 optimal weight:    0.2980
   chunk 55 optimal weight:    0.0010
   chunk 39 optimal weight:    0.9990
   chunk 33 optimal weight:    0.3980
   chunk 62 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 58 optimal weight:    5.9990
   chunk 69 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.4386

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

Flipped N/Q/H residues before XYZ refinement:
A 150 ASN
A 170 ASN
A 191 GLN
A 250 ASN
B 191 GLN
B 250 ASN
** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 191 GLN
C 250 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.183845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.153152 restraints weight = 8267.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.151247 restraints weight = 13446.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.152171 restraints weight = 10011.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.3157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5952  Z= 0.173
  Angle     :  0.542   8.346   8187  Z= 0.292
  Chirality :  0.044   0.223    948
  Planarity :  0.004   0.026   1032
  Dihedral  :  6.895  97.523   1038
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 13.91 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.29), residues: 783
  helix:  2.10 (0.36), residues: 210
  sheet:  1.07 (0.34), residues: 195
  loop : -1.09 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 153 
 HIS   0.010   0.001   HIS B 295 
 PHE   0.028   0.002   PHE A 115 
 TYR   0.016   0.001   TYR A 195 
 ARG   0.004   0.001   ARG A 117 

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 LEU cc_start: 0.8618 (mp) cc_final: 0.8385 (mp)
REVERT: A  106 ARG cc_start: 0.8654 (ttp-110) cc_final: 0.8117 (tmm-80)
REVERT: B   82 TYR cc_start: 0.7192 (p90) cc_final: 0.6715 (p90)
REVERT: C  168 TYR cc_start: 0.7607 (t80) cc_final: 0.7310 (t80)
  outliers start: 15
  outliers final: 10
  residues processed: 110
  average time/residue: 0.1741
  time to fit residues: 24.9666
Evaluate side-chains
  90 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  170 ASN
Chi-restraints excluded: chain C residue  307 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 9 optimal weight:    7.9990
   chunk 75 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 21 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
C 130 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.178629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.147205 restraints weight = 8426.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.145842 restraints weight = 11303.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.146069 restraints weight = 9884.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.3689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5952  Z= 0.262
  Angle     :  0.549   8.433   8187  Z= 0.295
  Chirality :  0.043   0.212    948
  Planarity :  0.004   0.024   1032
  Dihedral  :  6.667  93.765   1038
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 15.45 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.30), residues: 783
  helix:  1.97 (0.36), residues: 210
  sheet:  0.95 (0.36), residues: 189
  loop : -1.05 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 127 
 HIS   0.006   0.001   HIS B 295 
 PHE   0.025   0.002   PHE A 115 
 TYR   0.019   0.002   TYR C 195 
 ARG   0.006   0.001   ARG A 117 

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
REVERT: B   82 TYR cc_start: 0.7201 (p90) cc_final: 0.6808 (p90)
  outliers start: 17
  outliers final: 11
  residues processed: 97
  average time/residue: 0.1874
  time to fit residues: 23.6164
Evaluate side-chains
  86 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  302 HIS
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue  170 ASN
Chi-restraints excluded: chain C residue  307 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0020
   chunk 66 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 54 optimal weight:   10.0000
   overall best weight:    0.7190

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

Flipped N/Q/H residues before XYZ refinement:
A 108 GLN
B 295 HIS
C 130 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.180051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.148949 restraints weight = 8356.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.146732 restraints weight = 11513.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.147635 restraints weight = 9279.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.3875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   5952  Z= 0.206
  Angle     :  0.553   8.568   8187  Z= 0.289
  Chirality :  0.044   0.259    948
  Planarity :  0.003   0.023   1032
  Dihedral  :  6.603  91.628   1038
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 17.44 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.30), residues: 783
  helix:  2.10 (0.38), residues: 204
  sheet:  0.89 (0.37), residues: 189
  loop : -0.98 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  64 
 HIS   0.006   0.001   HIS B 295 
 PHE   0.026   0.002   PHE A 115 
 TYR   0.021   0.001   TYR C 195 
 ARG   0.004   0.001   ARG C 305 

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 LEU cc_start: 0.8870 (mp) cc_final: 0.8669 (mt)
REVERT: A  106 ARG cc_start: 0.8802 (ttp-110) cc_final: 0.8185 (tmm-80)
REVERT: B   82 TYR cc_start: 0.7182 (p90) cc_final: 0.6786 (p90)
REVERT: C  305 ARG cc_start: 0.7633 (mmt90) cc_final: 0.7319 (tpp-160)
  outliers start: 11
  outliers final: 10
  residues processed: 91
  average time/residue: 0.2215
  time to fit residues: 25.9306
Evaluate side-chains
  85 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  307 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0980
   chunk 62 optimal weight:    4.9990
   chunk 67 optimal weight:    0.2980
   chunk 69 optimal weight:    0.1980
   chunk 52 optimal weight:   10.0000
   chunk 14 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
C 130 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.181604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.150422 restraints weight = 8304.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.148589 restraints weight = 11739.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.149206 restraints weight = 9893.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.4195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   5952  Z= 0.161
  Angle     :  0.524   8.600   8187  Z= 0.274
  Chirality :  0.043   0.197    948
  Planarity :  0.003   0.023   1032
  Dihedral  :  6.285  86.391   1038
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 17.00 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.30), residues: 783
  helix:  2.21 (0.38), residues: 207
  sheet:  0.96 (0.43), residues: 147
  loop : -0.89 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 180 
 HIS   0.004   0.001   HIS C 295 
 PHE   0.025   0.002   PHE A 115 
 TYR   0.023   0.001   TYR B 195 
 ARG   0.006   0.001   ARG B 305 

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ARG cc_start: 0.8832 (ttp-110) cc_final: 0.8112 (tmm-80)
REVERT: A  208 HIS cc_start: 0.7118 (m90) cc_final: 0.6792 (m90)
REVERT: B   66 LEU cc_start: 0.8550 (mp) cc_final: 0.8266 (mt)
REVERT: B   82 TYR cc_start: 0.7266 (p90) cc_final: 0.6940 (p90)
  outliers start: 12
  outliers final: 10
  residues processed: 88
  average time/residue: 0.1992
  time to fit residues: 22.5943
Evaluate side-chains
  82 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  170 ASN
Chi-restraints excluded: chain C residue  307 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0980
   chunk 14 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0970
   chunk 49 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.5178

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.181620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.150834 restraints weight = 8290.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.149314 restraints weight = 9409.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.149786 restraints weight = 8476.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.4312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   5952  Z= 0.167
  Angle     :  0.526   8.543   8187  Z= 0.272
  Chirality :  0.043   0.197    948
  Planarity :  0.003   0.024   1032
  Dihedral  :  6.161  83.121   1038
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 18.10 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.31), residues: 783
  helix:  2.19 (0.38), residues: 207
  sheet:  0.99 (0.38), residues: 189
  loop : -0.87 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 180 
 HIS   0.003   0.001   HIS C 295 
 PHE   0.027   0.002   PHE A 115 
 TYR   0.023   0.001   TYR A 195 
 ARG   0.003   0.000   ARG A 117 

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
REVERT: A  106 ARG cc_start: 0.8811 (ttp-110) cc_final: 0.8064 (tmm-80)
REVERT: A  208 HIS cc_start: 0.7066 (m90) cc_final: 0.6791 (m90)
REVERT: A  304 GLU cc_start: 0.7881 (tt0) cc_final: 0.7628 (tp30)
REVERT: B   66 LEU cc_start: 0.8593 (mp) cc_final: 0.8327 (mt)
REVERT: B   82 TYR cc_start: 0.7241 (p90) cc_final: 0.6952 (p90)
  outliers start: 10
  outliers final: 9
  residues processed: 84
  average time/residue: 0.2001
  time to fit residues: 21.6744
Evaluate side-chains
  80 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  170 ASN
Chi-restraints excluded: chain C residue  307 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 64 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 77 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 60 optimal weight:   10.0000
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.179985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.149233 restraints weight = 8188.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.148132 restraints weight = 9068.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.148255 restraints weight = 8406.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.4548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5952  Z= 0.206
  Angle     :  0.542   8.497   8187  Z= 0.281
  Chirality :  0.043   0.178    948
  Planarity :  0.003   0.028   1032
  Dihedral  :  6.039  78.882   1038
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.81 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 18.98 %
    Favored  : 78.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.31), residues: 783
  helix:  2.08 (0.39), residues: 207
  sheet:  0.97 (0.38), residues: 189
  loop : -0.93 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 180 
 HIS   0.004   0.001   HIS C 295 
 PHE   0.028   0.002   PHE A 115 
 TYR   0.024   0.002   TYR C 195 
 ARG   0.003   0.001   ARG A 305 

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 TYR cc_start: 0.9389 (t80) cc_final: 0.8822 (t80)
REVERT: A  106 ARG cc_start: 0.8757 (ttp-110) cc_final: 0.7808 (tmm-80)
REVERT: A  208 HIS cc_start: 0.7071 (m90) cc_final: 0.6805 (m90)
REVERT: A  304 GLU cc_start: 0.8061 (tt0) cc_final: 0.7744 (tp30)
REVERT: B   66 LEU cc_start: 0.8645 (mp) cc_final: 0.8373 (mt)
REVERT: B   82 TYR cc_start: 0.7308 (p90) cc_final: 0.6994 (p90)
REVERT: B  255 TRP cc_start: 0.8425 (t60) cc_final: 0.8102 (t60)
  outliers start: 12
  outliers final: 10
  residues processed: 87
  average time/residue: 0.2008
  time to fit residues: 22.4323
Evaluate side-chains
  84 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  170 ASN
Chi-restraints excluded: chain C residue  307 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.180384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.149416 restraints weight = 8267.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.148254 restraints weight = 8784.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.148290 restraints weight = 8592.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.4692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5952  Z= 0.189
  Angle     :  0.534   8.349   8187  Z= 0.276
  Chirality :  0.043   0.201    948
  Planarity :  0.003   0.025   1032
  Dihedral  :  5.862  73.441   1038
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.43 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 19.21 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.30), residues: 783
  helix:  2.03 (0.39), residues: 207
  sheet:  0.99 (0.44), residues: 147
  loop : -0.91 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 180 
 HIS   0.004   0.001   HIS C 295 
 PHE   0.028   0.002   PHE A 115 
 TYR   0.024   0.001   TYR C 195 
 ARG   0.003   0.000   ARG A 117 

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 TYR cc_start: 0.9400 (t80) cc_final: 0.8890 (t80)
REVERT: A  106 ARG cc_start: 0.8755 (ttp-110) cc_final: 0.7837 (tmm-80)
REVERT: A  304 GLU cc_start: 0.7773 (tt0) cc_final: 0.7518 (tp30)
REVERT: B   82 TYR cc_start: 0.7327 (p90) cc_final: 0.7008 (p90)
REVERT: B  255 TRP cc_start: 0.8378 (t60) cc_final: 0.8081 (t60)
REVERT: C  304 GLU cc_start: 0.8279 (tp30) cc_final: 0.7969 (tp30)
  outliers start: 8
  outliers final: 7
  residues processed: 91
  average time/residue: 0.1746
  time to fit residues: 21.0728
Evaluate side-chains
  86 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain C residue  170 ASN
Chi-restraints excluded: chain C residue  307 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 34 optimal weight:    8.9990
   chunk 21 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 74 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 8 optimal weight:    9.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.0982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.176783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 104)---------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.145057 restraints weight = 8466.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.142738 restraints weight = 8888.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.144373 restraints weight = 7621.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.4849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5952  Z= 0.246
  Angle     :  0.557   8.135   8187  Z= 0.292
  Chirality :  0.044   0.175    948
  Planarity :  0.004   0.028   1032
  Dihedral  :  5.824  69.836   1038
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.55 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 18.98 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.30), residues: 783
  helix:  1.82 (0.39), residues: 207
  sheet:  0.92 (0.44), residues: 147
  loop : -0.98 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 180 
 HIS   0.004   0.001   HIS A 183 
 PHE   0.029   0.002   PHE A 115 
 TYR   0.024   0.002   TYR C 195 
 ARG   0.002   0.001   ARG A 117 

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 TYR cc_start: 0.9411 (t80) cc_final: 0.8873 (t80)
REVERT: A  106 ARG cc_start: 0.8759 (ttp-110) cc_final: 0.7841 (tmm-80)
REVERT: B   82 TYR cc_start: 0.7344 (p90) cc_final: 0.7042 (p90)
REVERT: B  102 TYR cc_start: 0.9344 (t80) cc_final: 0.9068 (t80)
REVERT: B  255 TRP cc_start: 0.8391 (t60) cc_final: 0.8063 (t60)
  outliers start: 8
  outliers final: 7
  residues processed: 90
  average time/residue: 0.1566
  time to fit residues: 18.9986
Evaluate side-chains
  75 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain C residue  170 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0030
   chunk 36 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 2 optimal weight:    8.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.6792

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.178757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.149345 restraints weight = 8441.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.147231 restraints weight = 12632.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.148195 restraints weight = 11250.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.4927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5952  Z= 0.192
  Angle     :  0.541   8.065   8187  Z= 0.281
  Chirality :  0.043   0.185    948
  Planarity :  0.003   0.025   1032
  Dihedral  :  5.687  66.769   1038
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.17 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 21.19 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.30), residues: 783
  helix:  1.87 (0.39), residues: 207
  sheet:  0.96 (0.44), residues: 147
  loop : -0.97 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 180 
 HIS   0.005   0.001   HIS C 302 
 PHE   0.031   0.002   PHE C 115 
 TYR   0.022   0.001   TYR C 195 
 ARG   0.006   0.001   ARG A 305 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1829.80 seconds
wall clock time: 33 minutes 49.05 seconds (2029.05 seconds total)