Starting phenix.real_space_refine
on Tue Jan 14 02:10:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ur5_42482/01_2025/8ur5_42482.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ur5_42482/01_2025/8ur5_42482.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ur5_42482/01_2025/8ur5_42482.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ur5_42482/01_2025/8ur5_42482.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ur5_42482/01_2025/8ur5_42482.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ur5_42482/01_2025/8ur5_42482.cif"
  }
  resolution = 3.7
  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=   0.013 sd=   0.124
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    3282      2.51       5
     N     858      2.21       5
     O     831      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 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: 4989
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1607
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 84}
          Link IDs: {'PTRANS': 14, 'TRANS': 217}
          Unresolved non-hydrogen bonds: 238
          Unresolved non-hydrogen angles: 293
          Unresolved non-hydrogen dihedrals: 185
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 11, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 150
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 3.01, per 1000 atoms: 0.60
  Number of scatterers: 4989
  At special positions: 0
  Unit cell: (87.1141, 82.8298, 74.2612, 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     831      8.00
     N     858      7.00
     C    3282      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=2.01
    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=2.05

  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 163 "
      " NAG A 502 " - " ASN A 129 "
      " NAG A 503 " - " ASN A  58 "
      " NAG A 504 " - " ASN A  91 "
      " NAG B 501 " - " ASN B 163 "
      " NAG B 502 " - " ASN B 129 "
      " NAG B 503 " - " ASN B  58 "
      " NAG B 504 " - " ASN B  91 "
      " NAG C 501 " - " ASN C 163 "
      " NAG C 502 " - " ASN C 129 "
      " NAG C 503 " - " ASN C  58 "
      " NAG C 504 " - " ASN C  91 "
  Time building additional restraints: 1.23
  Conformation dependent library (CDL) restraints added in 670.5 milliseconds
  

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1284

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 15 sheets defined
      16.8% alpha, 28.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 60 through 67
    Processing helix  chain 'A' and resid 101 through 106
    Processing helix  chain 'A' and resid 122 through 127
      removed outlier: 3.996A  pdb=" N   TRP A 127 " --> pdb=" O   LYS A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 196
    Processing helix  chain 'A' and resid 275 through 283
    Processing helix  chain 'B' and resid 60 through 67
    Processing helix  chain 'B' and resid 101 through 106
    Processing helix  chain 'B' and resid 122 through 127
      removed outlier: 3.996A  pdb=" N   TRP B 127 " --> pdb=" O   LYS B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 196
    Processing helix  chain 'B' and resid 275 through 283
    Processing helix  chain 'C' and resid 60 through 67
    Processing helix  chain 'C' and resid 101 through 106
    Processing helix  chain 'C' and resid 122 through 127
      removed outlier: 3.997A  pdb=" N   TRP C 127 " --> pdb=" O   LYS C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 187 through 196
    Processing helix  chain 'C' and resid 275 through 283
    Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54
    Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 119
      removed outlier: 6.625A  pdb=" N   TYR A 256 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   LEU A 179 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU A 175 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   LEU A 179 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 119
      removed outlier: 6.625A  pdb=" N   TYR A 256 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   LEU A 179 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU A 175 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 141
    Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 169
    Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 54
    Processing sheet with id=AA7, first strand: chain 'B' and resid 115 through 119
      removed outlier: 6.625A  pdb=" N   TYR B 256 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   LEU B 179 " --> pdb=" O   TYR B 256 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU B 175 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   LEU B 179 " --> pdb=" O   PRO B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 119
      removed outlier: 6.625A  pdb=" N   TYR B 256 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   LEU B 179 " --> pdb=" O   TYR B 256 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU B 175 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 140 through 141
    Processing sheet with id=AB1, first strand: chain 'B' and resid 164 through 169
    Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54
    Processing sheet with id=AB3, first strand: chain 'C' and resid 115 through 119
      removed outlier: 6.624A  pdb=" N   TYR C 256 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   LEU C 179 " --> pdb=" O   TYR C 256 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLU C 175 " --> pdb=" O   LEU C 260 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   LEU C 179 " --> pdb=" O   PRO C 254 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 115 through 119
      removed outlier: 6.624A  pdb=" N   TYR C 256 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   LEU C 179 " --> pdb=" O   TYR C 256 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLU C 175 " --> pdb=" O   LEU C 260 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 140 through 141
    Processing sheet with id=AB6, first strand: chain 'C' and resid 164 through 169

    189 hydrogen bonds defined for protein.
    531 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: 1.29

  Time building geometry restraints manager: 1.41 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 753
        1.31 -     1.44: 1533
        1.44 -     1.57: 2841
        1.57 -     1.69: 9
        1.69 -     1.82: 18
  Bond restraints: 5154
  Sorted by residual:
  bond pdb=" C   ARG C 229 "
       pdb=" O   ARG C 229 "
    ideal  model  delta    sigma   weight residual
    1.234  1.185  0.048 1.24e-02 6.50e+03 1.53e+01
  bond pdb=" C   ARG B 229 "
       pdb=" O   ARG B 229 "
    ideal  model  delta    sigma   weight residual
    1.234  1.186  0.048 1.24e-02 6.50e+03 1.47e+01
  bond pdb=" C   ARG A 229 "
       pdb=" O   ARG A 229 "
    ideal  model  delta    sigma   weight residual
    1.234  1.187  0.047 1.24e-02 6.50e+03 1.45e+01
  bond pdb=" CA  ARG B 229 "
       pdb=" CB  ARG B 229 "
    ideal  model  delta    sigma   weight residual
    1.533  1.474  0.059 1.66e-02 3.63e+03 1.26e+01
  bond pdb=" CA  ARG A 229 "
       pdb=" CB  ARG A 229 "
    ideal  model  delta    sigma   weight residual
    1.533  1.474  0.059 1.66e-02 3.63e+03 1.26e+01
  ... (remaining 5149 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 5765
        1.56 -     3.11: 1047
        3.11 -     4.67: 169
        4.67 -     6.23: 93
        6.23 -     7.79: 45
  Bond angle restraints: 7119
  Sorted by residual:
  angle pdb=" C   HIS B 184 "
        pdb=" N   PRO B 185 "
        pdb=" CA  PRO B 185 "
      ideal   model   delta    sigma   weight residual
     119.66  126.85   -7.19 7.30e-01 1.88e+00 9.71e+01
  angle pdb=" C   HIS A 184 "
        pdb=" N   PRO A 185 "
        pdb=" CA  PRO A 185 "
      ideal   model   delta    sigma   weight residual
     119.66  126.82   -7.16 7.30e-01 1.88e+00 9.63e+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  126.80   -7.14 7.30e-01 1.88e+00 9.56e+01
  angle pdb=" C   ASN A  88 "
        pdb=" N   PRO A  89 "
        pdb=" CA  PRO A  89 "
      ideal   model   delta    sigma   weight residual
     119.85  126.77   -6.92 1.01e+00 9.80e-01 4.70e+01
  angle pdb=" C   ASN B  88 "
        pdb=" N   PRO B  89 "
        pdb=" CA  PRO B  89 "
      ideal   model   delta    sigma   weight residual
     119.85  126.76   -6.91 1.01e+00 9.80e-01 4.68e+01
  ... (remaining 7114 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.28: 2848
       12.28 -    24.55: 111
       24.55 -    36.83: 55
       36.83 -    49.10: 14
       49.10 -    61.38: 5
  Dihedral angle restraints: 3033
    sinusoidal: 1020
      harmonic: 2013
  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  130.38  -37.38     1      1.00e+01 1.00e-02 1.97e+01
  dihedral pdb=" SG  CYS A 107 "
           pdb=" CB  CYS A 271 "
           pdb=" SG  CYS A 271 "
           pdb=" CA  CYS A 271 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00  -11.62  -61.38     1      2.00e+01 2.50e-03 1.25e+01
  dihedral pdb=" N   ARG C 229 "
           pdb=" C   ARG C 229 "
           pdb=" CA  ARG C 229 "
           pdb=" CB  ARG C 229 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  114.36    8.44     0      2.50e+00 1.60e-01 1.14e+01
  ... (remaining 3030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 529
       0.067 -    0.133: 230
       0.133 -    0.200: 27
       0.200 -    0.267: 33
       0.267 -    0.334: 15
  Chirality restraints: 834
  Sorted by residual:
  chirality pdb=" C2  NAG B 501 "
            pdb=" C1  NAG B 501 "
            pdb=" C3  NAG B 501 "
            pdb=" N2  NAG B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.83    0.33 2.00e-01 2.50e+01 2.78e+00
  chirality pdb=" C2  NAG C 501 "
            pdb=" C1  NAG C 501 "
            pdb=" C3  NAG C 501 "
            pdb=" N2  NAG C 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.83    0.33 2.00e-01 2.50e+01 2.78e+00
  chirality pdb=" C2  NAG A 501 "
            pdb=" C1  NAG A 501 "
            pdb=" C3  NAG A 501 "
            pdb=" N2  NAG A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.82    0.33 2.00e-01 2.50e+01 2.76e+00
  ... (remaining 831 not shown)

  Planarity restraints: 912
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C  92 "   -0.014 2.00e-02 2.50e+03   2.89e-02 8.38e+00
        pdb=" C   GLY C  92 "    0.050 2.00e-02 2.50e+03
        pdb=" O   GLY C  92 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   THR C  93 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  92 "   -0.014 2.00e-02 2.50e+03   2.89e-02 8.35e+00
        pdb=" C   GLY A  92 "    0.050 2.00e-02 2.50e+03
        pdb=" O   GLY A  92 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   THR A  93 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B  92 "    0.014 2.00e-02 2.50e+03   2.88e-02 8.31e+00
        pdb=" C   GLY B  92 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   GLY B  92 "    0.019 2.00e-02 2.50e+03
        pdb=" N   THR B  93 "    0.017 2.00e-02 2.50e+03
  ... (remaining 909 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 30
        2.59 -     3.17: 3891
        3.17 -     3.74: 7195
        3.74 -     4.32: 10290
        4.32 -     4.90: 16277
  Nonbonded interactions: 37683
  Sorted by model distance:
  nonbonded pdb=" SG  CYS B  59 "
            pdb=" SG  CYS B  71 "
     model   vdw
     2.011 3.760
  nonbonded pdb=" SG  CYS C  59 "
            pdb=" SG  CYS C  71 "
     model   vdw
     2.011 3.760
  nonbonded pdb=" SG  CYS C  94 "
            pdb=" SG  CYS C 139 "
     model   vdw
     2.020 3.760
  nonbonded pdb=" SG  CYS B  94 "
            pdb=" SG  CYS B 139 "
     model   vdw
     2.020 3.760
  nonbonded pdb=" SG  CYS C 107 "
            pdb=" SG  CYS C 271 "
     model   vdw
     2.046 3.760
  ... (remaining 37678 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain '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:             0.430
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.340
  Find NCS groups from input model:        0.100
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
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      :  0.011   0.060   5154  Z= 0.742
  Angle     :  1.447   7.787   7119  Z= 1.011
  Chirality :  0.089   0.334    834
  Planarity :  0.005   0.029    900
  Dihedral  :  9.297  51.962   1740
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.35 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  3.42 %
    Favored  : 94.87 %
  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: -0.71 (0.29), residues: 690
  helix: -2.02 (0.42), residues: 117
  sheet:  2.31 (0.34), residues: 171
  loop : -1.32 (0.26), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP B  80 
 HIS   0.004   0.001   HIS C 130 
 PHE   0.010   0.002   PHE C 115 
 TYR   0.027   0.004   TYR B 195 
 ARG   0.002   0.001   ARG A 229 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 166
  time to evaluate  : 0.572 
Fit side-chains
REVERT: A  229 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7726 (mtm110)
REVERT: A  230 ILE cc_start: 0.9278 (tt) cc_final: 0.9013 (tt)
REVERT: A  256 TYR cc_start: 0.8142 (m-80) cc_final: 0.7753 (m-10)
REVERT: B  229 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7723 (mtm110)
REVERT: B  256 TYR cc_start: 0.7999 (m-80) cc_final: 0.7524 (m-10)
REVERT: C  155 THR cc_start: 0.6919 (p) cc_final: 0.6688 (t)
REVERT: C  229 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7594 (mtm110)
REVERT: C  256 TYR cc_start: 0.7957 (m-80) cc_final: 0.7540 (m-10)
  outliers start: 6
  outliers final: 1
  residues processed: 170
  average time/residue: 0.2207
  time to fit residues: 45.3683
Evaluate side-chains
  106 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 102
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain A residue  229 ARG
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain C residue  229 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 17 optimal weight:    0.4980
   chunk 35 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.6988

-------------------------------------------------------------------------------
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 = 0.3897 r_free = 0.3897 target = 0.164792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.130269 restraints weight = 7906.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.129623 restraints weight = 8957.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.131934 restraints weight = 7175.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.2968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5154  Z= 0.307
  Angle     :  0.715   7.410   7119  Z= 0.366
  Chirality :  0.055   0.640    834
  Planarity :  0.005   0.025    900
  Dihedral  :  6.942  58.278   1012
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.48 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 19.09 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -0.17 (0.31), residues: 690
  helix: -1.61 (0.46), residues: 117
  sheet:  1.79 (0.35), residues: 180
  loop : -0.54 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 153 
 HIS   0.005   0.001   HIS C 184 
 PHE   0.025   0.002   PHE C 147 
 TYR   0.017   0.002   TYR B  82 
 ARG   0.003   0.001   ARG C 224 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.626 
Fit side-chains
REVERT: A  229 ARG cc_start: 0.8316 (ttm170) cc_final: 0.7864 (mtm110)
REVERT: A  243 ILE cc_start: 0.8647 (tp) cc_final: 0.8440 (tt)
REVERT: A  256 TYR cc_start: 0.8452 (m-80) cc_final: 0.7924 (m-10)
REVERT: B  191 GLN cc_start: 0.8068 (tp40) cc_final: 0.7449 (tp40)
REVERT: B  229 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7698 (mtm110)
REVERT: B  256 TYR cc_start: 0.8478 (m-80) cc_final: 0.7948 (m-10)
REVERT: C  118 PHE cc_start: 0.7234 (p90) cc_final: 0.7020 (p90)
REVERT: C  155 THR cc_start: 0.7319 (p) cc_final: 0.6803 (t)
REVERT: C  229 ARG cc_start: 0.8695 (ttm170) cc_final: 0.7707 (mtm110)
REVERT: C  256 TYR cc_start: 0.8277 (m-80) cc_final: 0.7852 (m-10)
  outliers start: 12
  outliers final: 9
  residues processed: 123
  average time/residue: 0.2145
  time to fit residues: 32.5858
Evaluate side-chains
  108 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  107 CYS
Chi-restraints excluded: chain C residue  236 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 23 optimal weight:   10.0000
   chunk 63 optimal weight:    8.9990
   chunk 49 optimal weight:    5.9990
   chunk 10 optimal weight:    0.5980
   chunk 54 optimal weight:   20.0000
   chunk 13 optimal weight:    0.0570
   chunk 14 optimal weight:    1.9990
   chunk 42 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    1.5304

-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.161773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.127354 restraints weight = 8056.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.129034 restraints weight = 7925.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.130202 restraints weight = 6032.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.3517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5154  Z= 0.256
  Angle     :  0.646   6.730   7119  Z= 0.326
  Chirality :  0.050   0.520    834
  Planarity :  0.004   0.026    900
  Dihedral  :  5.848  53.427   1003
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.91 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 20.80 %
    Favored  : 74.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.31), residues: 690
  helix: -1.33 (0.48), residues: 114
  sheet:  1.19 (0.35), residues: 198
  loop : -0.47 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C  64 
 HIS   0.004   0.001   HIS C 196 
 PHE   0.016   0.002   PHE C 147 
 TYR   0.016   0.002   TYR C  82 
 ARG   0.002   0.001   ARG C 262 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.569 
Fit side-chains
REVERT: A  229 ARG cc_start: 0.8372 (ttm170) cc_final: 0.7890 (mtm110)
REVERT: A  243 ILE cc_start: 0.8705 (tp) cc_final: 0.8457 (tt)
REVERT: A  256 TYR cc_start: 0.8622 (m-80) cc_final: 0.8058 (m-10)
REVERT: B  172 LYS cc_start: 0.8743 (mmmt) cc_final: 0.8534 (mttp)
REVERT: B  191 GLN cc_start: 0.8190 (tp40) cc_final: 0.7421 (tp40)
REVERT: B  229 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7377 (mtm110)
REVERT: B  256 TYR cc_start: 0.8580 (m-80) cc_final: 0.7499 (m-10)
REVERT: C   80 TRP cc_start: 0.8926 (p90) cc_final: 0.8276 (p90)
REVERT: C  118 PHE cc_start: 0.7132 (p90) cc_final: 0.6912 (p90)
REVERT: C  229 ARG cc_start: 0.8708 (ttm170) cc_final: 0.7668 (mtm110)
REVERT: C  256 TYR cc_start: 0.8357 (m-80) cc_final: 0.8089 (m-10)
  outliers start: 16
  outliers final: 12
  residues processed: 112
  average time/residue: 0.2266
  time to fit residues: 31.3974
Evaluate side-chains
  111 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain B residue   59 CYS
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  107 CYS
Chi-restraints excluded: chain C residue  164 LEU
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 44 optimal weight:    9.9990
   chunk 5 optimal weight:    0.7980
   chunk 38 optimal weight:    5.9990
   chunk 49 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0870
   chunk 13 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 7 optimal weight:    0.3980
   overall best weight:    0.5760

-------------------------------------------------------------------------------
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 = 0.3887 r_free = 0.3887 target = 0.163403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.130277 restraints weight = 8155.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.130277 restraints weight = 8998.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.130277 restraints weight = 8997.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
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      :  0.002   0.024   5154  Z= 0.150
  Angle     :  0.578   6.788   7119  Z= 0.288
  Chirality :  0.049   0.531    834
  Planarity :  0.004   0.025    900
  Dihedral  :  5.615  46.567   1003
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.49 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 22.51 %
    Favored  : 72.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.07 (0.32), residues: 690
  helix: -0.88 (0.50), residues: 114
  sheet:  1.14 (0.35), residues: 198
  loop : -0.38 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  64 
 HIS   0.005   0.001   HIS C 196 
 PHE   0.016   0.002   PHE A 118 
 TYR   0.019   0.002   TYR C 232 
 ARG   0.003   0.000   ARG B 106 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
REVERT: A  191 GLN cc_start: 0.8324 (tp40) cc_final: 0.7842 (tp40)
REVERT: A  229 ARG cc_start: 0.8296 (ttm170) cc_final: 0.7619 (mtm110)
REVERT: A  256 TYR cc_start: 0.8465 (m-80) cc_final: 0.7903 (m-10)
REVERT: B  191 GLN cc_start: 0.8384 (tp40) cc_final: 0.7580 (tp40)
REVERT: B  229 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.6866 (mtm110)
REVERT: C   80 TRP cc_start: 0.8793 (p90) cc_final: 0.8264 (p90)
REVERT: C  118 PHE cc_start: 0.6964 (p90) cc_final: 0.6607 (p90)
REVERT: C  229 ARG cc_start: 0.8613 (ttm170) cc_final: 0.7724 (mtm110)
REVERT: C  256 TYR cc_start: 0.8251 (m-80) cc_final: 0.7853 (m-10)
  outliers start: 19
  outliers final: 12
  residues processed: 127
  average time/residue: 0.2138
  time to fit residues: 33.6043
Evaluate side-chains
  114 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain B residue   59 CYS
Chi-restraints excluded: chain B residue   71 CYS
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  107 CYS
Chi-restraints excluded: chain C residue  236 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 44 optimal weight:   10.0000
   chunk 39 optimal weight:    0.8980
   chunk 37 optimal weight:    9.9990
   chunk 8 optimal weight:    1.9990
   chunk 59 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 52 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 196 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.157249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.121430 restraints weight = 8252.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.121218 restraints weight = 8611.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.123253 restraints weight = 7199.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.4344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   5154  Z= 0.346
  Angle     :  0.640   9.227   7119  Z= 0.322
  Chirality :  0.052   0.546    834
  Planarity :  0.004   0.034    900
  Dihedral  :  5.937  46.385   1003
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.06 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  7.12 %
    Allowed  : 23.36 %
    Favored  : 69.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.31), residues: 690
  helix: -1.34 (0.48), residues: 114
  sheet:  0.95 (0.36), residues: 180
  loop : -0.43 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 153 
 HIS   0.005   0.001   HIS C 196 
 PHE   0.016   0.002   PHE B 118 
 TYR   0.017   0.002   TYR B 168 
 ARG   0.008   0.001   ARG A 224 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  237 LEU cc_start: 0.8973 (mt) cc_final: 0.8728 (mt)
REVERT: B  191 GLN cc_start: 0.8563 (tp40) cc_final: 0.7681 (tp40)
REVERT: B  229 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.6890 (mtm110)
REVERT: C   80 TRP cc_start: 0.8890 (p90) cc_final: 0.8398 (p90)
REVERT: C  118 PHE cc_start: 0.7151 (p90) cc_final: 0.6855 (p90)
REVERT: C  229 ARG cc_start: 0.8648 (ttm170) cc_final: 0.7704 (mtm110)
REVERT: C  256 TYR cc_start: 0.8358 (m-80) cc_final: 0.8074 (m-10)
  outliers start: 25
  outliers final: 17
  residues processed: 110
  average time/residue: 0.2091
  time to fit residues: 28.3176
Evaluate side-chains
  110 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain B residue   59 CYS
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   71 CYS
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  182 VAL
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 48 optimal weight:    0.6980
   chunk 33 optimal weight:    6.9990
   chunk 67 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0170
   chunk 26 optimal weight:    0.0970
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.7620

-------------------------------------------------------------------------------
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 = 0.3835 r_free = 0.3835 target = 0.159315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.125789 restraints weight = 8138.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.125531 restraints weight = 8101.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.126760 restraints weight = 7044.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.4543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5154  Z= 0.165
  Angle     :  0.614  11.135   7119  Z= 0.298
  Chirality :  0.050   0.447    834
  Planarity :  0.004   0.034    900
  Dihedral  :  5.776  42.560   1003
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  4.49 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 25.93 %
    Favored  : 69.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.19 (0.31), residues: 690
  helix: -0.87 (0.50), residues: 114
  sheet:  0.99 (0.37), residues: 180
  loop : -0.38 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  64 
 HIS   0.005   0.001   HIS C 196 
 PHE   0.018   0.002   PHE B 118 
 TYR   0.027   0.001   TYR B 168 
 ARG   0.005   0.001   ARG A 224 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ASN cc_start: 0.6090 (t0) cc_final: 0.5873 (t0)
REVERT: A   64 TRP cc_start: 0.8909 (OUTLIER) cc_final: 0.8474 (t-100)
REVERT: B  168 TYR cc_start: 0.7719 (t80) cc_final: 0.7312 (t80)
REVERT: B  191 GLN cc_start: 0.8606 (tp40) cc_final: 0.7746 (tp40)
REVERT: B  229 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.6493 (mtm110)
REVERT: C   80 TRP cc_start: 0.8783 (p90) cc_final: 0.8377 (p90)
REVERT: C  191 GLN cc_start: 0.8580 (tp40) cc_final: 0.7636 (tp40)
REVERT: C  229 ARG cc_start: 0.8616 (ttm170) cc_final: 0.7623 (mtm110)
  outliers start: 17
  outliers final: 12
  residues processed: 107
  average time/residue: 0.2024
  time to fit residues: 26.9060
Evaluate side-chains
  107 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 TRP
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain B residue   59 CYS
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   71 CYS
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 25 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9990
   chunk 11 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 48 optimal weight:    0.5980
   chunk 10 optimal weight:    7.9990
   chunk 21 optimal weight:    4.9990
   chunk 67 optimal weight:    8.9990
   overall best weight:    2.5188

-------------------------------------------------------------------------------
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 = 0.3781 r_free = 0.3781 target = 0.154710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.118817 restraints weight = 8174.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.118968 restraints weight = 8428.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.120112 restraints weight = 6637.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.4885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   5154  Z= 0.383
  Angle     :  0.663  11.989   7119  Z= 0.331
  Chirality :  0.050   0.386    834
  Planarity :  0.004   0.036    900
  Dihedral  :  6.112  43.614   1003
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  4.20 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  6.27 %
    Allowed  : 25.36 %
    Favored  : 68.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.31), residues: 690
  helix: -0.93 (0.49), residues: 108
  sheet:  0.73 (0.38), residues: 180
  loop : -0.59 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 127 
 HIS   0.006   0.001   HIS C 196 
 PHE   0.017   0.002   PHE A 118 
 TYR   0.022   0.002   TYR B 168 
 ARG   0.013   0.001   ARG A 224 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8986 (OUTLIER) cc_final: 0.8567 (t-100)
REVERT: A  229 ARG cc_start: 0.8360 (ttm170) cc_final: 0.7162 (mtm-85)
REVERT: B  191 GLN cc_start: 0.8545 (tp40) cc_final: 0.7616 (tp40)
REVERT: B  229 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.6607 (mtm110)
REVERT: B  232 TYR cc_start: 0.8729 (m-80) cc_final: 0.8314 (m-10)
REVERT: C   80 TRP cc_start: 0.8902 (p90) cc_final: 0.8457 (p90)
REVERT: C  229 ARG cc_start: 0.8680 (ttm170) cc_final: 0.7637 (mtm110)
  outliers start: 22
  outliers final: 13
  residues processed: 99
  average time/residue: 0.2131
  time to fit residues: 25.9356
Evaluate side-chains
  100 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 TRP
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   71 CYS
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  120 ILE
Chi-restraints excluded: chain C residue  182 VAL
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0980
   chunk 1 optimal weight:    0.0270
   chunk 4 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.5642

-------------------------------------------------------------------------------
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 = 0.3830 r_free = 0.3830 target = 0.159195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.125575 restraints weight = 8145.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.124950 restraints weight = 8541.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.126876 restraints weight = 7716.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.4968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5154  Z= 0.160
  Angle     :  0.650  11.495   7119  Z= 0.315
  Chirality :  0.048   0.356    834
  Planarity :  0.004   0.037    900
  Dihedral  :  6.123  54.164   1003
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  4.35 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 28.77 %
    Favored  : 66.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

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: -0.30 (0.31), residues: 690
  helix: -0.83 (0.50), residues: 111
  sheet:  0.81 (0.38), residues: 180
  loop : -0.44 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 127 
 HIS   0.006   0.001   HIS C 196 
 PHE   0.020   0.002   PHE B 118 
 TYR   0.034   0.002   TYR C 168 
 ARG   0.005   0.001   ARG A 106 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8931 (OUTLIER) cc_final: 0.8542 (t-100)
REVERT: A  229 ARG cc_start: 0.8318 (ttm170) cc_final: 0.7216 (mtm-85)
REVERT: B  168 TYR cc_start: 0.8349 (t80) cc_final: 0.7842 (t80)
REVERT: B  191 GLN cc_start: 0.8471 (tp40) cc_final: 0.7585 (tp40)
REVERT: B  229 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.6501 (mtm110)
REVERT: C   80 TRP cc_start: 0.8799 (p90) cc_final: 0.8434 (p90)
REVERT: C  229 ARG cc_start: 0.8601 (ttm170) cc_final: 0.7312 (mtm-85)
  outliers start: 15
  outliers final: 11
  residues processed: 97
  average time/residue: 0.2107
  time to fit residues: 25.2724
Evaluate side-chains
  94 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   64 TRP
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   71 CYS
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 37 optimal weight:   10.0000
   chunk 35 optimal weight:    2.9990
   chunk 34 optimal weight:    9.9990
   chunk 39 optimal weight:    7.9990
   chunk 57 optimal weight:    7.9990
   chunk 15 optimal weight:    6.9990
   chunk 62 optimal weight:    3.9990
   chunk 25 optimal weight:   10.0000
   chunk 61 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    3.7588

-------------------------------------------------------------------------------
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 = 0.3753 r_free = 0.3753 target = 0.152482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.119595 restraints weight = 8158.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.117764 restraints weight = 7959.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.119433 restraints weight = 7952.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.5309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.053   5154  Z= 0.539
  Angle     :  0.748  12.611   7119  Z= 0.379
  Chirality :  0.051   0.289    834
  Planarity :  0.005   0.038    900
  Dihedral  :  6.113  43.595   1003
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  :  4.93 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 29.06 %
    Favored  : 65.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.30), residues: 690
  helix: -1.60 (0.46), residues: 105
  sheet:  0.52 (0.40), residues: 174
  loop : -0.94 (0.27), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP C 153 
 HIS   0.008   0.002   HIS B 183 
 PHE   0.021   0.003   PHE A 118 
 TYR   0.033   0.003   TYR C 168 
 ARG   0.007   0.001   ARG B 224 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8989 (OUTLIER) cc_final: 0.8586 (t-100)
REVERT: B  191 GLN cc_start: 0.8592 (tp40) cc_final: 0.7600 (tp40)
REVERT: B  229 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.6620 (mtm110)
REVERT: C  120 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8496 (tt)
REVERT: C  229 ARG cc_start: 0.8720 (ttm170) cc_final: 0.7428 (mtm-85)
  outliers start: 19
  outliers final: 12
  residues processed: 93
  average time/residue: 0.2208
  time to fit residues: 25.3048
Evaluate side-chains
  104 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ASN
Chi-restraints excluded: chain A residue   64 TRP
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   71 CYS
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  120 ILE
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 46 optimal weight:    8.9990
   chunk 22 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0070
   chunk 50 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 23 optimal weight:    8.9990
   overall best weight:    0.7000

-------------------------------------------------------------------------------
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 = 0.3815 r_free = 0.3815 target = 0.157803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.121278 restraints weight = 8174.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.121274 restraints weight = 8342.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.123499 restraints weight = 7281.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.5378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   5154  Z= 0.165
  Angle     :  0.632  11.475   7119  Z= 0.306
  Chirality :  0.046   0.233    834
  Planarity :  0.004   0.051    900
  Dihedral  :  5.545  40.587   1003
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  :  4.06 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 31.34 %
    Favored  : 64.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

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: -0.75 (0.30), residues: 690
  helix: -0.83 (0.51), residues: 105
  sheet:  0.55 (0.39), residues: 180
  loop : -0.89 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  64 
 HIS   0.005   0.001   HIS C 196 
 PHE   0.022   0.002   PHE A 118 
 TYR   0.031   0.002   TYR C 168 
 ARG   0.013   0.001   ARG A 224 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8950 (OUTLIER) cc_final: 0.8518 (t-100)
REVERT: B  168 TYR cc_start: 0.8381 (t80) cc_final: 0.8163 (t80)
REVERT: B  191 GLN cc_start: 0.8566 (tp40) cc_final: 0.7689 (tp40)
REVERT: B  196 HIS cc_start: 0.8575 (m90) cc_final: 0.8282 (m90)
REVERT: B  229 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.6439 (mtm110)
REVERT: B  232 TYR cc_start: 0.8671 (m-80) cc_final: 0.8376 (m-10)
REVERT: C  229 ARG cc_start: 0.8672 (ttm170) cc_final: 0.7234 (mtm-85)
  outliers start: 14
  outliers final: 10
  residues processed: 103
  average time/residue: 0.2337
  time to fit residues: 30.4884
Evaluate side-chains
  95 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 TRP
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   71 CYS
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 55 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0770
   chunk 40 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 65 optimal weight:    8.9990
   overall best weight:    0.7940

-------------------------------------------------------------------------------
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 = 0.3824 r_free = 0.3824 target = 0.158489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.125350 restraints weight = 8084.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.124466 restraints weight = 9652.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.126335 restraints weight = 7484.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.5571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5154  Z= 0.173
  Angle     :  0.617  10.461   7119  Z= 0.299
  Chirality :  0.046   0.188    834
  Planarity :  0.004   0.054    900
  Dihedral  :  5.401  42.967   1003
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  :  3.33 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 31.34 %
    Favored  : 65.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

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: -0.70 (0.31), residues: 690
  helix: -1.05 (0.50), residues: 114
  sheet:  0.66 (0.39), residues: 180
  loop : -0.79 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C  80 
 HIS   0.005   0.001   HIS C 196 
 PHE   0.022   0.002   PHE B 118 
 TYR   0.027   0.002   TYR C 168 
 ARG   0.013   0.001   ARG A 224 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1786.16 seconds
wall clock time: 33 minutes 16.27 seconds (1996.27 seconds total)