Starting phenix.real_space_refine
on Thu Mar  6 05:41:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ur5_42482/03_2025/8ur5_42482.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ur5_42482/03_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_42482/03_2025/8ur5_42482.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ur5_42482/03_2025/8ur5_42482.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ur5_42482/03_2025/8ur5_42482.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ur5_42482/03_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-5624/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: 3.49, per 1000 atoms: 0.70
  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=9, 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
    Simple disulfide: pdb=" SG  CYS C  59 " - pdb=" SG  CYS C  71 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B  59 " - pdb=" SG  CYS B  71 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C  94 " - pdb=" SG  CYS C 139 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  94 " - pdb=" SG  CYS B 139 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 107 " - pdb=" SG  CYS C 271 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 107 " - pdb=" SG  CYS B 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 779.7 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: 0.86
  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: 2.12

  Time building geometry restraints manager: 1.47 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: 2852
       12.28 -    24.55: 115
       24.55 -    36.83: 57
       36.83 -    49.10: 18
       49.10 -    61.38: 9
  Dihedral angle restraints: 3051
    sinusoidal: 1038
      harmonic: 2013
  Sorted by residual:
  dihedral pdb=" CB  CYS B  94 "
           pdb=" SG  CYS B  94 "
           pdb=" SG  CYS B 139 "
           pdb=" CB  CYS B 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.41  -37.41     1      1.00e+01 1.00e-02 1.97e+01
  dihedral pdb=" CB  CYS C  94 "
           pdb=" SG  CYS C  94 "
           pdb=" SG  CYS C 139 "
           pdb=" CB  CYS C 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.40  -37.40     1      1.00e+01 1.00e-02 1.97e+01
  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
  ... (remaining 3048 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:
        2.51 -     2.99: 2582
        2.99 -     3.47: 4265
        3.47 -     3.94: 7952
        3.94 -     4.42: 8647
        4.42 -     4.90: 14219
  Nonbonded interactions: 37665
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 163 "
            pdb=" N2  NAG B 501 "
     model   vdw
     2.510 3.120
  nonbonded pdb=" OD1 ASN A 163 "
            pdb=" N2  NAG A 501 "
     model   vdw
     2.510 3.120
  nonbonded pdb=" OD1 ASN C 163 "
            pdb=" N2  NAG C 501 "
     model   vdw
     2.510 3.120
  nonbonded pdb=" O   ILE A 275 "
            pdb=" N   GLU A 278 "
     model   vdw
     2.541 3.120
  nonbonded pdb=" O   ILE B 275 "
            pdb=" N   GLU B 278 "
     model   vdw
     2.541 3.120
  ... (remaining 37660 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: 0.06
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:             17.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.470
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.060
  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:5.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.470
-------------------------------------------------------------------------------
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= 0.725
  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 : 2.510

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  : 1.019 
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: 0.2761
  time to fit residues: 58.0662
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  : 0.623 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 54 optimal weight:    0.0010
   chunk 20 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.0790

-------------------------------------------------------------------------------
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 = 0.3931 r_free = 0.3931 target = 0.166672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.133520 restraints weight = 8110.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.132908 restraints weight = 6601.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.134486 restraints weight = 5394.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   5154  Z= 0.252
  Angle     :  0.704   8.048   7119  Z= 0.361
  Chirality :  0.054   0.628    834
  Planarity :  0.005   0.022    900
  Dihedral  :  7.040  57.451   1012
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.33 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 18.80 %
    Favored  : 77.21 %
  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:  0.01 (0.31), residues: 690
  helix: -1.35 (0.48), residues: 117
  sheet:  1.92 (0.35), residues: 180
  loop : -0.47 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 153 
 HIS   0.004   0.001   HIS C 184 
 PHE   0.025   0.002   PHE C 147 
 TYR   0.016   0.002   TYR B  82 
 ARG   0.002   0.000   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
  133 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.868 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.8347 (t80) cc_final: 0.7998 (t80)
REVERT: A  224 ARG cc_start: 0.8085 (mmm-85) cc_final: 0.7498 (ttm170)
REVERT: A  229 ARG cc_start: 0.8326 (ttm170) cc_final: 0.7776 (mtm110)
REVERT: A  237 LEU cc_start: 0.8853 (mt) cc_final: 0.8638 (mt)
REVERT: A  243 ILE cc_start: 0.8640 (tp) cc_final: 0.8376 (tt)
REVERT: A  256 TYR cc_start: 0.8625 (m-80) cc_final: 0.8137 (m-10)
REVERT: B  191 GLN cc_start: 0.7969 (tp40) cc_final: 0.7461 (tp40)
REVERT: B  229 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7842 (mtm110)
REVERT: B  256 TYR cc_start: 0.8500 (m-80) cc_final: 0.7971 (m-10)
REVERT: C  155 THR cc_start: 0.7332 (p) cc_final: 0.6799 (t)
REVERT: C  229 ARG cc_start: 0.8744 (ttm170) cc_final: 0.7754 (mtm110)
REVERT: C  256 TYR cc_start: 0.8333 (m-80) cc_final: 0.7957 (m-10)
  outliers start: 14
  outliers final: 7
  residues processed: 129
  average time/residue: 0.3591
  time to fit residues: 59.5245
Evaluate side-chains
  109 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   65 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  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:    1.9990
   chunk 49 optimal weight:    0.0020
   chunk 10 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    1.3394

-------------------------------------------------------------------------------
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 = 0.3890 r_free = 0.3890 target = 0.164222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.129903 restraints weight = 8065.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.130541 restraints weight = 7833.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.131290 restraints weight = 6641.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.3506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5154  Z= 0.243
  Angle     :  0.659   6.897   7119  Z= 0.335
  Chirality :  0.053   0.581    834
  Planarity :  0.004   0.025    900
  Dihedral  :  5.988  51.907   1003
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.48 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 19.94 %
    Favored  : 74.93 %
  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: -0.04 (0.31), residues: 690
  helix: -1.15 (0.49), residues: 117
  sheet:  1.35 (0.35), residues: 198
  loop : -0.37 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C  80 
 HIS   0.004   0.001   HIS C 196 
 PHE   0.024   0.002   PHE C 118 
 TYR   0.018   0.002   TYR C  82 
 ARG   0.006   0.001   ARG B 106 

*********************** 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
  127 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.791 
Fit side-chains
REVERT: A  229 ARG cc_start: 0.8334 (ttm170) cc_final: 0.7830 (mtm110)
REVERT: A  237 LEU cc_start: 0.8941 (mt) cc_final: 0.8733 (mt)
REVERT: A  256 TYR cc_start: 0.8601 (m-80) cc_final: 0.8044 (m-10)
REVERT: B   66 LEU cc_start: 0.9182 (mp) cc_final: 0.8960 (mp)
REVERT: B  191 GLN cc_start: 0.8198 (tp40) cc_final: 0.7458 (tp40)
REVERT: B  229 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7464 (mtm110)
REVERT: B  256 TYR cc_start: 0.8562 (m-80) cc_final: 0.7484 (m-10)
REVERT: C   80 TRP cc_start: 0.8866 (p90) cc_final: 0.8304 (p90)
REVERT: C  152 LEU cc_start: 0.7887 (mt) cc_final: 0.7557 (mt)
REVERT: C  229 ARG cc_start: 0.8715 (ttm170) cc_final: 0.7703 (mtm110)
REVERT: C  256 TYR cc_start: 0.8336 (m-80) cc_final: 0.7914 (m-10)
  outliers start: 18
  outliers final: 10
  residues processed: 120
  average time/residue: 0.2780
  time to fit residues: 43.0228
Evaluate side-chains
  117 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  155 THR
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   56 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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 44 optimal weight:    6.9990
   chunk 5 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0970
   chunk 6 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 13 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.3582

-------------------------------------------------------------------------------
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 = 0.3870 r_free = 0.3870 target = 0.162298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.128734 restraints weight = 8205.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.129529 restraints weight = 8678.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.130343 restraints weight = 6791.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.3930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5154  Z= 0.236
  Angle     :  0.618   7.722   7119  Z= 0.310
  Chirality :  0.052   0.504    834
  Planarity :  0.004   0.026    900
  Dihedral  :  5.836  47.680   1003
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.93 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  6.55 %
    Allowed  : 19.66 %
    Favored  : 73.79 %
  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: -0.09 (0.31), residues: 690
  helix: -1.03 (0.50), residues: 114
  sheet:  1.02 (0.35), residues: 195
  loop : -0.26 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 153 
 HIS   0.005   0.001   HIS C 196 
 PHE   0.024   0.002   PHE C 118 
 TYR   0.035   0.002   TYR C 232 
 ARG   0.005   0.001   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
  129 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 ARG cc_start: 0.8345 (ttm170) cc_final: 0.7617 (mtm110)
REVERT: A  237 LEU cc_start: 0.8948 (mt) cc_final: 0.8684 (mt)
REVERT: A  256 TYR cc_start: 0.8531 (m-80) cc_final: 0.7974 (m-10)
REVERT: B   66 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8900 (mp)
REVERT: B  191 GLN cc_start: 0.8347 (tp40) cc_final: 0.7547 (tp40)
REVERT: B  229 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.6958 (mtm110)
REVERT: C   80 TRP cc_start: 0.8824 (p90) cc_final: 0.8208 (p90)
REVERT: C  229 ARG cc_start: 0.8622 (ttm170) cc_final: 0.7685 (mtm110)
REVERT: C  256 TYR cc_start: 0.8312 (m-80) cc_final: 0.7884 (m-10)
  outliers start: 23
  outliers final: 14
  residues processed: 122
  average time/residue: 0.2413
  time to fit residues: 37.2936
Evaluate side-chains
  116 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
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  282 LEU
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  155 THR
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  282 LEU
Chi-restraints excluded: chain C residue   65 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 44 optimal weight:   10.0000
   chunk 39 optimal weight:    6.9990
   chunk 37 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   chunk 52 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9980
   chunk 15 optimal weight:    0.3980
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 = 0.3846 r_free = 0.3846 target = 0.160395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.127252 restraints weight = 8278.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.128165 restraints weight = 8668.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.128814 restraints weight = 6404.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.4315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5154  Z= 0.246
  Angle     :  0.620   8.149   7119  Z= 0.311
  Chirality :  0.050   0.487    834
  Planarity :  0.004   0.026    900
  Dihedral  :  5.997  44.593   1003
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.77 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  7.41 %
    Allowed  : 19.94 %
    Favored  : 72.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.46 %

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: -0.89 (0.51), residues: 114
  sheet:  0.74 (0.35), residues: 195
  loop : -0.27 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  64 
 HIS   0.006   0.001   HIS C 196 
 PHE   0.024   0.002   PHE C 118 
 TYR   0.034   0.002   TYR C 232 
 ARG   0.004   0.001   ARG B 106 

*********************** 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
  124 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.562 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 ARG cc_start: 0.8230 (ttm170) cc_final: 0.7615 (mtm110)
REVERT: A  237 LEU cc_start: 0.9003 (mt) cc_final: 0.8707 (mt)
REVERT: B   66 LEU cc_start: 0.9202 (mp) cc_final: 0.8971 (mp)
REVERT: B  168 TYR cc_start: 0.8328 (t80) cc_final: 0.7977 (t80)
REVERT: B  191 GLN cc_start: 0.8531 (tp40) cc_final: 0.7643 (tp40)
REVERT: B  229 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.6797 (mtm110)
REVERT: C   80 TRP cc_start: 0.8740 (p90) cc_final: 0.8316 (p90)
REVERT: C  229 ARG cc_start: 0.8645 (ttm170) cc_final: 0.7714 (mtm110)
REVERT: C  256 TYR cc_start: 0.8317 (m-80) cc_final: 0.8111 (m-10)
  outliers start: 26
  outliers final: 17
  residues processed: 113
  average time/residue: 0.3249
  time to fit residues: 45.5148
Evaluate side-chains
  113 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 1.556 
-------------------------------------------------------------------------------
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  205 VAL
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue   64 TRP
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 B residue  282 LEU
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  164 LEU
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  244 ILE
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:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 67 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 9 optimal weight:    8.9990
   chunk 2 optimal weight:    0.0270
   chunk 26 optimal weight:    0.0570
   chunk 62 optimal weight:    6.9990
   overall best weight:    2.8162

-------------------------------------------------------------------------------
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 = 0.3795 r_free = 0.3795 target = 0.155941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.120478 restraints weight = 8306.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.120984 restraints weight = 8211.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.122675 restraints weight = 6307.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.4723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   5154  Z= 0.422
  Angle     :  0.695   8.524   7119  Z= 0.351
  Chirality :  0.051   0.425    834
  Planarity :  0.004   0.031    900
  Dihedral  :  6.426  45.765   1003
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  4.64 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  7.12 %
    Allowed  : 22.51 %
    Favored  : 70.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.46 %

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: -0.57 (0.31), residues: 690
  helix: -1.27 (0.49), residues: 114
  sheet:  0.64 (0.37), residues: 180
  loop : -0.54 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 153 
 HIS   0.005   0.001   HIS C 196 
 PHE   0.027   0.003   PHE C 118 
 TYR   0.042   0.002   TYR C 232 
 ARG   0.008   0.001   ARG B 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
  116 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 91
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8934 (OUTLIER) cc_final: 0.8519 (t-100)
REVERT: A  229 ARG cc_start: 0.8355 (ttm170) cc_final: 0.7577 (mtm110)
REVERT: A  237 LEU cc_start: 0.9062 (mt) cc_final: 0.8721 (mt)
REVERT: B   66 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8944 (mp)
REVERT: B  168 TYR cc_start: 0.8455 (t80) cc_final: 0.7952 (t80)
REVERT: B  191 GLN cc_start: 0.8665 (tp40) cc_final: 0.7751 (tp40)
REVERT: B  229 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.6616 (mtm110)
REVERT: B  232 TYR cc_start: 0.8795 (m-80) cc_final: 0.8540 (m-10)
REVERT: C   80 TRP cc_start: 0.8874 (p90) cc_final: 0.8363 (p90)
REVERT: C  172 LYS cc_start: 0.8982 (mtpp) cc_final: 0.8621 (mttp)
REVERT: C  229 ARG cc_start: 0.8718 (ttm170) cc_final: 0.7697 (mtm110)
REVERT: C  274 HIS cc_start: 0.8301 (OUTLIER) cc_final: 0.7914 (t-90)
  outliers start: 25
  outliers final: 18
  residues processed: 106
  average time/residue: 0.2118
  time to fit residues: 27.8447
Evaluate side-chains
  113 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
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   65 ILE
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   66 LEU
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 B residue  282 LEU
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  164 LEU
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  244 ILE
Chi-restraints excluded: chain C residue  274 HIS
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:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 48 optimal weight:    0.5980
   chunk 10 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 67 optimal weight:    7.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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 = 0.158764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.125408 restraints weight = 8045.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.125849 restraints weight = 8691.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.127415 restraints weight = 6750.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.4827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5154  Z= 0.242
  Angle     :  0.673   9.305   7119  Z= 0.334
  Chirality :  0.051   0.476    834
  Planarity :  0.004   0.038    900
  Dihedral  :  6.110  45.389   1003
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  4.35 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 25.64 %
    Favored  : 68.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.46 %

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 (0.31), residues: 690
  helix: -0.61 (0.53), residues: 108
  sheet:  0.61 (0.37), residues: 180
  loop : -0.65 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 180 
 HIS   0.005   0.001   HIS C 196 
 PHE   0.021   0.002   PHE B 118 
 TYR   0.028   0.002   TYR C 232 
 ARG   0.008   0.001   ARG B 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
  115 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8920 (OUTLIER) cc_final: 0.8517 (t-100)
REVERT: A  237 LEU cc_start: 0.9061 (mt) cc_final: 0.8711 (mt)
REVERT: B   66 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8902 (mp)
REVERT: B  168 TYR cc_start: 0.8445 (t80) cc_final: 0.7950 (t80)
REVERT: B  191 GLN cc_start: 0.8605 (tp40) cc_final: 0.7581 (tp40)
REVERT: B  229 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.6617 (mtm110)
REVERT: B  232 TYR cc_start: 0.8720 (m-80) cc_final: 0.8400 (m-10)
REVERT: C   80 TRP cc_start: 0.8810 (p90) cc_final: 0.8395 (p90)
REVERT: C  172 LYS cc_start: 0.8944 (mtpp) cc_final: 0.8626 (mttp)
REVERT: C  229 ARG cc_start: 0.8661 (ttm170) cc_final: 0.7618 (mtm110)
REVERT: C  256 TYR cc_start: 0.8360 (m-80) cc_final: 0.8143 (m-10)
REVERT: C  274 HIS cc_start: 0.8274 (OUTLIER) cc_final: 0.8023 (t-90)
  outliers start: 20
  outliers final: 13
  residues processed: 107
  average time/residue: 0.2949
  time to fit residues: 39.5774
Evaluate side-chains
  107 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
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  188 ILE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   66 LEU
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 B residue  282 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  274 HIS
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:    9.9990
   chunk 9 optimal weight:    7.9990
   chunk 29 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0980
   chunk 4 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0010
   chunk 68 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.5786

-------------------------------------------------------------------------------
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 = 0.3847 r_free = 0.3847 target = 0.160776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 133)---------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.121914 restraints weight = 8219.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.123557 restraints weight = 6309.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.125071 restraints weight = 5364.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.5045

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= 0.168
  Angle     :  0.614   7.683   7119  Z= 0.302
  Chirality :  0.046   0.197    834
  Planarity :  0.004   0.041    900
  Dihedral  :  5.700  47.952   1003
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  4.20 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 25.64 %
    Favored  : 69.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.61 %

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: -0.39 (0.31), residues: 690
  helix: -0.56 (0.53), residues: 105
  sheet:  0.70 (0.37), residues: 180
  loop : -0.59 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 127 
 HIS   0.006   0.001   HIS C 196 
 PHE   0.020   0.002   PHE B 118 
 TYR   0.025   0.001   TYR A 168 
 ARG   0.011   0.001   ARG B 224 

*********************** 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
  107 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8899 (OUTLIER) cc_final: 0.8536 (t-100)
REVERT: A  237 LEU cc_start: 0.9181 (mt) cc_final: 0.8890 (mt)
REVERT: B   66 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8960 (mp)
REVERT: B  168 TYR cc_start: 0.8466 (t80) cc_final: 0.7861 (t80)
REVERT: B  191 GLN cc_start: 0.8363 (tp40) cc_final: 0.7453 (tp40)
REVERT: B  229 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.6481 (mtm110)
REVERT: B  232 TYR cc_start: 0.8756 (m-80) cc_final: 0.8529 (m-10)
REVERT: C   80 TRP cc_start: 0.8744 (p90) cc_final: 0.8468 (p90)
REVERT: C  172 LYS cc_start: 0.8906 (mtpp) cc_final: 0.8571 (mttp)
REVERT: C  229 ARG cc_start: 0.8651 (ttm170) cc_final: 0.7276 (mtm-85)
REVERT: C  256 TYR cc_start: 0.8358 (m-80) cc_final: 0.8053 (m-10)
REVERT: C  274 HIS cc_start: 0.7771 (OUTLIER) cc_final: 0.6712 (t70)
  outliers start: 17
  outliers final: 9
  residues processed: 99
  average time/residue: 0.2257
  time to fit residues: 27.6377
Evaluate side-chains
  99 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 TRP
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   66 LEU
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 B residue  282 LEU
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  274 HIS
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:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 34 optimal weight:    9.9990
   chunk 39 optimal weight:    4.9990
   chunk 57 optimal weight:    0.0040
   chunk 15 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   overall best weight:    2.1998

-------------------------------------------------------------------------------
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 = 0.3818 r_free = 0.3818 target = 0.157867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.122348 restraints weight = 8054.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.122895 restraints weight = 8826.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.123567 restraints weight = 6399.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.5220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   5154  Z= 0.334
  Angle     :  0.645   6.787   7119  Z= 0.327
  Chirality :  0.047   0.247    834
  Planarity :  0.004   0.049    900
  Dihedral  :  5.780  46.243   1003
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  :  4.20 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 27.64 %
    Favored  : 68.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.61 %

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: -0.61 (0.31), residues: 690
  helix: -0.69 (0.53), residues: 105
  sheet:  0.58 (0.38), residues: 180
  loop : -0.76 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 153 
 HIS   0.006   0.001   HIS C 196 
 PHE   0.019   0.002   PHE A 118 
 TYR   0.025   0.002   TYR C 232 
 ARG   0.011   0.001   ARG A 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
  108 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8937 (OUTLIER) cc_final: 0.8575 (t-100)
REVERT: A  229 ARG cc_start: 0.8411 (ttm170) cc_final: 0.7202 (mtm-85)
REVERT: A  237 LEU cc_start: 0.9109 (mt) cc_final: 0.8745 (mt)
REVERT: B   66 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8923 (mp)
REVERT: B  168 TYR cc_start: 0.8525 (t80) cc_final: 0.7694 (t80)
REVERT: B  191 GLN cc_start: 0.8528 (tp40) cc_final: 0.7503 (tp40)
REVERT: B  229 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.6563 (mtm110)
REVERT: B  232 TYR cc_start: 0.8768 (m-80) cc_final: 0.8420 (m-10)
REVERT: C   80 TRP cc_start: 0.8831 (p90) cc_final: 0.8465 (p90)
REVERT: C  229 ARG cc_start: 0.8693 (ttm170) cc_final: 0.7354 (mtm-85)
REVERT: C  256 TYR cc_start: 0.8278 (m-80) cc_final: 0.8022 (m-10)
REVERT: C  274 HIS cc_start: 0.7866 (OUTLIER) cc_final: 0.6850 (t70)
  outliers start: 15
  outliers final: 10
  residues processed: 102
  average time/residue: 0.2783
  time to fit residues: 35.9764
Evaluate side-chains
  104 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
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  188 ILE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   66 LEU
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 B residue  282 LEU
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  274 HIS
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:    9.9990
   chunk 22 optimal weight:    0.7980
   chunk 16 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 17 optimal weight:    0.4980
   chunk 50 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 23 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 = 0.3845 r_free = 0.3845 target = 0.159411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.124436 restraints weight = 8411.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.124430 restraints weight = 9169.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.125856 restraints weight = 7942.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.5350

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= 0.184
  Angle     :  0.608   7.859   7119  Z= 0.300
  Chirality :  0.045   0.195    834
  Planarity :  0.004   0.041    900
  Dihedral  :  5.472  44.545   1003
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  :  3.91 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 28.21 %
    Favored  : 67.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.61 %

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: -0.52 (0.31), residues: 690
  helix: -0.61 (0.54), residues: 105
  sheet:  0.67 (0.38), residues: 180
  loop : -0.73 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 127 
 HIS   0.005   0.001   HIS C 196 
 PHE   0.023   0.002   PHE B 118 
 TYR   0.024   0.001   TYR A 168 
 ARG   0.010   0.001   ARG B 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
  109 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8924 (OUTLIER) cc_final: 0.8557 (t-100)
REVERT: A  229 ARG cc_start: 0.8440 (ttm170) cc_final: 0.7140 (mtm-85)
REVERT: A  237 LEU cc_start: 0.9210 (mt) cc_final: 0.8877 (mt)
REVERT: B   66 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8960 (mp)
REVERT: B  168 TYR cc_start: 0.8584 (t80) cc_final: 0.7835 (t80)
REVERT: B  191 GLN cc_start: 0.8439 (tp40) cc_final: 0.7511 (tp40)
REVERT: B  229 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.6144 (mtm110)
REVERT: B  232 TYR cc_start: 0.8765 (m-80) cc_final: 0.8534 (m-10)
REVERT: C   80 TRP cc_start: 0.8776 (p90) cc_final: 0.8476 (p90)
REVERT: C  152 LEU cc_start: 0.7829 (mt) cc_final: 0.7446 (mt)
REVERT: C  172 LYS cc_start: 0.8973 (mtpp) cc_final: 0.8640 (mttp)
REVERT: C  229 ARG cc_start: 0.8665 (ttm170) cc_final: 0.7155 (mtm-85)
REVERT: C  274 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.6816 (t70)
  outliers start: 15
  outliers final: 9
  residues processed: 102
  average time/residue: 0.2245
  time to fit residues: 28.2150
Evaluate side-chains
  103 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 TRP
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   66 LEU
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 B residue  282 LEU
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  274 HIS
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:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    9.9990
   chunk 22 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 23 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 65 optimal weight:    7.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.3801 r_free = 0.3801 target = 0.156166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.123275 restraints weight = 8207.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.123480 restraints weight = 8259.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.125359 restraints weight = 7574.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.5512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   5154  Z= 0.386
  Angle     :  0.672   7.916   7119  Z= 0.341
  Chirality :  0.048   0.231    834
  Planarity :  0.004   0.044    900
  Dihedral  :  5.810  44.638   1003
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  :  4.93 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 26.50 %
    Favored  : 68.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.61 %

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: -0.77 (0.31), residues: 690
  helix: -0.99 (0.52), residues: 105
  sheet:  0.52 (0.38), residues: 180
  loop : -0.84 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 153 
 HIS   0.006   0.002   HIS B 183 
 PHE   0.022   0.003   PHE B 118 
 TYR   0.029   0.002   TYR C 232 
 ARG   0.011   0.001   ARG B 224 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2435.03 seconds
wall clock time: 45 minutes 35.55 seconds (2735.55 seconds total)