Starting phenix.real_space_refine
on Sat Apr 26 19:45:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j7p_36045/04_2025/8j7p_36045.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j7p_36045/04_2025/8j7p_36045.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j7p_36045/04_2025/8j7p_36045.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j7p_36045/04_2025/8j7p_36045.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j7p_36045/04_2025/8j7p_36045.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j7p_36045/04_2025/8j7p_36045.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      21      5.16       5
     C    2082      2.51       5
     N     519      2.21       5
     O     636      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3258
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1086
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 2.24, per 1000 atoms: 0.69
  Number of scatterers: 3258
  At special positions: 0
  Unit cell: (99.6, 98.77, 36.52, 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      21     16.00
     O     636      8.00
     N     519      7.00
     C    2082      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 253 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 618.4 milliseconds
  

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  780

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 23.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 125 through 126
      removed outlier: 6.014A  pdb=" N   TYR B 125 " --> pdb=" O   ILE A 126 " (cutoff:3.500A)
      removed outlier: 6.001A  pdb=" N   TYR A 125 " --> pdb=" O   ILE C 126 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 129 through 130
      removed outlier: 6.702A  pdb=" N   LYS B 129 " --> pdb=" O   SER A 130 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   LYS A 129 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 133 through 137
      removed outlier: 6.487A  pdb=" N   SER B 134 " --> pdb=" O   TYR A 135 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   VAL A 137 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   ASP B 136 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   SER A 134 " --> pdb=" O   TYR C 135 " (cutoff:3.500A)
      removed outlier: 7.874A  pdb=" N   VAL C 137 " --> pdb=" O   SER A 134 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   ASP A 136 " --> pdb=" O   VAL C 137 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 144
      removed outlier: 6.555A  pdb=" N   ILE B 142 " --> pdb=" O   TYR A 143 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   ILE A 142 " --> pdb=" O   TYR C 143 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 151
    Processing sheet with id=AA6, first strand: chain 'B' and resid 154 through 157
    Processing sheet with id=AA7, first strand: chain 'B' and resid 163 through 164
    Processing sheet with id=AA8, first strand: chain 'B' and resid 167 through 168
    Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 175
      removed outlier: 8.065A  pdb=" N   LYS B 173 " --> pdb=" O   THR A 174 " (cutoff:3.500A)
      removed outlier: 8.047A  pdb=" N   LYS A 173 " --> pdb=" O   THR C 174 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 185 through 187
    Processing sheet with id=AB2, first strand: chain 'B' and resid 190 through 191
    Processing sheet with id=AB3, first strand: chain 'B' and resid 202 through 203
      removed outlier: 6.214A  pdb=" N   VAL B 202 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   VAL A 202 " --> pdb=" O   ILE C 203 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 210 through 211
    Processing sheet with id=AB5, first strand: chain 'B' and resid 222 through 230
      removed outlier: 6.971A  pdb=" N   ASN A 223 " --> pdb=" O   HIS B 222 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   ILE B 224 " --> pdb=" O   ASN A 223 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   VAL A 225 " --> pdb=" O   ILE B 224 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   LEU B 226 " --> pdb=" O   VAL A 225 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   MET A 227 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   MET B 228 " --> pdb=" O   MET A 227 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   GLN A 229 " --> pdb=" O   MET B 228 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   ASN C 223 " --> pdb=" O   HIS A 222 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   ILE A 224 " --> pdb=" O   ASN C 223 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   VAL C 225 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU A 226 " --> pdb=" O   VAL C 225 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   MET C 227 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   MET A 228 " --> pdb=" O   MET C 227 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   GLN C 229 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 242 through 244
      removed outlier: 6.419A  pdb=" N   GLN B 242 " --> pdb=" O   ILE A 243 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   GLN A 242 " --> pdb=" O   ILE C 243 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'B' and resid 251 through 252
      removed outlier: 6.434A  pdb=" N   VAL B 251 " --> pdb=" O   ASP A 252 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   VAL A 251 " --> pdb=" O   ASP C 252 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7

    22 hydrogen bonds defined for protein.
    66 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.78

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1026
        1.34 -     1.45: 478
        1.45 -     1.57: 1772
        1.57 -     1.68: 0
        1.68 -     1.80: 36
  Bond restraints: 3312
  Sorted by residual:
  bond pdb=" CA  ILE A 187 "
       pdb=" CB  ILE A 187 "
    ideal  model  delta    sigma   weight residual
    1.540  1.519  0.021 1.36e-02 5.41e+03 2.47e+00
  bond pdb=" CA  ILE B 187 "
       pdb=" CB  ILE B 187 "
    ideal  model  delta    sigma   weight residual
    1.540  1.520  0.020 1.36e-02 5.41e+03 2.25e+00
  bond pdb=" CA  ILE C 187 "
       pdb=" CB  ILE C 187 "
    ideal  model  delta    sigma   weight residual
    1.540  1.520  0.020 1.36e-02 5.41e+03 2.25e+00
  bond pdb=" C   MET A 192 "
       pdb=" N   LYS A 193 "
    ideal  model  delta    sigma   weight residual
    1.334  1.313  0.021 1.58e-02 4.01e+03 1.81e+00
  bond pdb=" C   MET C 192 "
       pdb=" N   LYS C 193 "
    ideal  model  delta    sigma   weight residual
    1.334  1.313  0.021 1.58e-02 4.01e+03 1.78e+00
  ... (remaining 3307 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 4052
        1.20 -     2.40: 372
        2.40 -     3.60: 52
        3.60 -     4.79: 21
        4.79 -     5.99: 6
  Bond angle restraints: 4503
  Sorted by residual:
  angle pdb=" C   LEU C 144 "
        pdb=" N   ASN C 145 "
        pdb=" CA  ASN C 145 "
      ideal   model   delta    sigma   weight residual
     121.54  127.26   -5.72 1.91e+00 2.74e-01 8.96e+00
  angle pdb=" C   LEU A 144 "
        pdb=" N   ASN A 145 "
        pdb=" CA  ASN A 145 "
      ideal   model   delta    sigma   weight residual
     121.54  127.25   -5.71 1.91e+00 2.74e-01 8.93e+00
  angle pdb=" C   LEU B 144 "
        pdb=" N   ASN B 145 "
        pdb=" CA  ASN B 145 "
      ideal   model   delta    sigma   weight residual
     121.54  127.24   -5.70 1.91e+00 2.74e-01 8.89e+00
  angle pdb=" C   GLN A 245 "
        pdb=" N   GLU A 246 "
        pdb=" CA  GLU A 246 "
      ideal   model   delta    sigma   weight residual
     122.36  117.75    4.61 1.60e+00 3.91e-01 8.31e+00
  angle pdb=" C   GLN C 245 "
        pdb=" N   GLU C 246 "
        pdb=" CA  GLU C 246 "
      ideal   model   delta    sigma   weight residual
     122.36  117.76    4.60 1.60e+00 3.91e-01 8.27e+00
  ... (remaining 4498 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.06: 1750
       14.06 -    28.11: 191
       28.11 -    42.17: 36
       42.17 -    56.22: 9
       56.22 -    70.28: 3
  Dihedral angle restraints: 1989
    sinusoidal: 771
      harmonic: 1218
  Sorted by residual:
  dihedral pdb=" CA  GLN B 138 "
           pdb=" C   GLN B 138 "
           pdb=" N   LYS B 139 "
           pdb=" CA  LYS B 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.28   24.72     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  GLN A 138 "
           pdb=" C   GLN A 138 "
           pdb=" N   LYS A 139 "
           pdb=" CA  LYS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.29   24.71     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  GLN C 138 "
           pdb=" C   GLN C 138 "
           pdb=" N   LYS C 139 "
           pdb=" CA  LYS C 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.30   24.70     0      5.00e+00 4.00e-02 2.44e+01
  ... (remaining 1986 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 252
       0.035 -    0.070: 176
       0.070 -    0.105: 75
       0.105 -    0.140: 37
       0.140 -    0.175: 3
  Chirality restraints: 543
  Sorted by residual:
  chirality pdb=" CA  ASN A 145 "
            pdb=" N   ASN A 145 "
            pdb=" C   ASN A 145 "
            pdb=" CB  ASN A 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.18 2.00e-01 2.50e+01 7.68e-01
  chirality pdb=" CA  ASN B 145 "
            pdb=" N   ASN B 145 "
            pdb=" C   ASN B 145 "
            pdb=" CB  ASN B 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.50e-01
  chirality pdb=" CA  ASN C 145 "
            pdb=" N   ASN C 145 "
            pdb=" C   ASN C 145 "
            pdb=" CB  ASN C 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.15e-01
  ... (remaining 540 not shown)

  Planarity restraints: 558
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 143 "    0.016 2.00e-02 2.50e+03   9.85e-03 1.94e+00
        pdb=" CG  TYR C 143 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 143 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 143 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 143 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 143 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 143 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR C 143 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 143 "    0.016 2.00e-02 2.50e+03   9.76e-03 1.90e+00
        pdb=" CG  TYR B 143 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 143 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 143 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 143 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 143 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 143 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 143 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 143 "    0.015 2.00e-02 2.50e+03   9.74e-03 1.90e+00
        pdb=" CG  TYR A 143 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 143 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 143 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 143 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 143 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 143 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 143 "    0.003 2.00e-02 2.50e+03
  ... (remaining 555 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 26
        2.60 -     3.18: 2874
        3.18 -     3.75: 4489
        3.75 -     4.33: 6662
        4.33 -     4.90: 12205
  Nonbonded interactions: 26256
  Sorted by model distance:
  nonbonded pdb=" SG  CYS A 214 "
            pdb=" SG  CYS A 253 "
     model   vdw
     2.025 3.760
  nonbonded pdb=" SG  CYS C 214 "
            pdb=" SG  CYS C 253 "
     model   vdw
     2.025 3.760
  nonbonded pdb=" CE1 TYR A 143 "
            pdb=" CD1 ILE A 146 "
     model   vdw
     2.402 3.760
  nonbonded pdb=" CE1 TYR C 143 "
            pdb=" CD1 ILE C 146 "
     model   vdw
     2.403 3.760
  nonbonded pdb=" OG1 THR A 233 "
            pdb=" N   THR A 234 "
     model   vdw
     2.404 3.120
  ... (remaining 26251 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 individual isotropic
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:             1.350
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.990
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  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:3.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.042   3313  Z= 0.419
  Angle     :  0.807   5.994   4505  Z= 0.458
  Chirality :  0.056   0.175    543
  Planarity :  0.003   0.011    558
  Dihedral  : 12.537  70.278   1206
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 16.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.04 %
    Favored  : 84.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  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: -5.75 (0.29), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.37 (0.22), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS A 239 
 PHE   0.010   0.003   PHE C 237 
 TYR   0.023   0.003   TYR C 143 
 ARG   0.002   0.000   ARG A 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18382 (   22)
  hydrogen bonds       : angle       9.09638 (   66)
  SS BOND              : bond        0.00613 (    1)
  SS BOND              : angle       0.87238 (    2)
  covalent geometry    : bond        0.00926 ( 3312)
  covalent geometry    : angle       0.80697 ( 4503)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.337 
Fit side-chains
REVERT: B  146 ILE cc_start: 0.8983 (pt) cc_final: 0.8697 (pt)
REVERT: B  161 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8075 (mm-30)
REVERT: B  207 MET cc_start: 0.7786 (mtm) cc_final: 0.5920 (mtm)
REVERT: B  235 THR cc_start: 0.8687 (m) cc_final: 0.8169 (p)
REVERT: A  146 ILE cc_start: 0.9005 (pt) cc_final: 0.8700 (pt)
REVERT: A  161 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8015 (mm-30)
REVERT: A  207 MET cc_start: 0.7985 (mtm) cc_final: 0.7196 (mmm)
REVERT: A  215 THR cc_start: 0.8543 (t) cc_final: 0.8298 (t)
REVERT: A  235 THR cc_start: 0.8525 (m) cc_final: 0.8126 (p)
REVERT: C  140 ARG cc_start: 0.8625 (mtt180) cc_final: 0.8414 (mtt-85)
REVERT: C  146 ILE cc_start: 0.8834 (pt) cc_final: 0.8610 (pt)
REVERT: C  161 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7552 (mm-30)
REVERT: C  220 LYS cc_start: 0.9160 (mttt) cc_final: 0.8785 (mttm)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1784
  time to fit residues: 16.3531
Evaluate side-chains
  73 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 10 optimal weight:    0.3980
   chunk 19 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 22 optimal weight:    8.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
B 156 ASN
B 222 HIS
B 229 GLN
A 155 ASN
A 156 ASN
A 223 ASN
C 155 ASN
C 156 ASN
C 223 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.146599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.125423 restraints weight = 3923.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3944 rms_B_bonded: 2.86
r_work: 0.3838 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3714 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.1798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3313  Z= 0.122
  Angle     :  0.600   6.358   4505  Z= 0.322
  Chirality :  0.053   0.175    543
  Planarity :  0.002   0.008    558
  Dihedral  :  6.320  20.121    447
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.02 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 11.90 %
    Favored  : 86.77 %
  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: -5.41 (0.30), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.12 (0.23), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS C 239 
 PHE   0.008   0.001   PHE B 237 
 TYR   0.012   0.001   TYR B 132 
 ARG   0.002   0.000   ARG B 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02419 (   22)
  hydrogen bonds       : angle       6.20745 (   66)
  SS BOND              : bond        0.00270 (    1)
  SS BOND              : angle       0.26649 (    2)
  covalent geometry    : bond        0.00270 ( 3312)
  covalent geometry    : angle       0.60056 ( 4503)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.362 
Fit side-chains
REVERT: B  129 LYS cc_start: 0.9094 (ptpt) cc_final: 0.8833 (ptmt)
REVERT: B  146 ILE cc_start: 0.8909 (pt) cc_final: 0.8663 (pt)
REVERT: B  170 GLN cc_start: 0.9215 (mp10) cc_final: 0.8950 (mp10)
REVERT: B  207 MET cc_start: 0.8286 (mtm) cc_final: 0.7045 (mtm)
REVERT: B  210 MET cc_start: 0.8827 (mtt) cc_final: 0.8623 (mtm)
REVERT: A  207 MET cc_start: 0.8440 (mtm) cc_final: 0.7607 (mmm)
REVERT: A  210 MET cc_start: 0.8656 (mtm) cc_final: 0.8427 (mtt)
REVERT: C  207 MET cc_start: 0.8350 (mtm) cc_final: 0.8118 (mtm)
REVERT: C  210 MET cc_start: 0.8366 (mtt) cc_final: 0.8068 (mtp)
REVERT: C  220 LYS cc_start: 0.9213 (mttt) cc_final: 0.8822 (mttm)
  outliers start: 5
  outliers final: 3
  residues processed: 96
  average time/residue: 0.1541
  time to fit residues: 17.9431
Evaluate side-chains
  83 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain C residue  128 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 14 optimal weight:    9.9990
   chunk 3 optimal weight:    7.9990
   chunk 19 optimal weight:    6.9990
   chunk 13 optimal weight:    8.9990
   chunk 34 optimal weight:    0.2980
   chunk 7 optimal weight:    3.9990
   chunk 8 optimal weight:    9.9990
   chunk 23 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   chunk 11 optimal weight:    0.3980
   overall best weight:    2.4584

-------------------------------------------------------------------------------
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 = 0.4094 r_free = 0.4094 target = 0.140881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.120021 restraints weight = 3998.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3871 rms_B_bonded: 2.85
r_work: 0.3743 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3616 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3313  Z= 0.182
  Angle     :  0.630   5.968   4505  Z= 0.344
  Chirality :  0.053   0.172    543
  Planarity :  0.002   0.009    558
  Dihedral  :  6.343  20.772    447
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.28 %
    Favored  : 89.72 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 13.49 %
    Favored  : 83.86 %
  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: -5.24 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.99 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS B 239 
 PHE   0.009   0.001   PHE B 237 
 TYR   0.023   0.002   TYR C 236 
 ARG   0.001   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02697 (   22)
  hydrogen bonds       : angle       5.88862 (   66)
  SS BOND              : bond        0.00400 (    1)
  SS BOND              : angle       0.55543 (    2)
  covalent geometry    : bond        0.00422 ( 3312)
  covalent geometry    : angle       0.63028 ( 4503)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.399 
Fit side-chains
REVERT: B  139 LYS cc_start: 0.9281 (mttt) cc_final: 0.9075 (mttp)
REVERT: B  146 ILE cc_start: 0.8955 (pt) cc_final: 0.8696 (pt)
REVERT: B  170 GLN cc_start: 0.9178 (mp10) cc_final: 0.8928 (mp10)
REVERT: B  210 MET cc_start: 0.8896 (mtt) cc_final: 0.8696 (mtm)
REVERT: A  207 MET cc_start: 0.8398 (mtm) cc_final: 0.8095 (mtm)
REVERT: A  210 MET cc_start: 0.8712 (mtm) cc_final: 0.8364 (mtp)
REVERT: C  210 MET cc_start: 0.8428 (mtt) cc_final: 0.8166 (mtp)
REVERT: C  220 LYS cc_start: 0.9183 (mttt) cc_final: 0.8806 (mttm)
  outliers start: 10
  outliers final: 9
  residues processed: 77
  average time/residue: 0.1701
  time to fit residues: 15.6786
Evaluate side-chains
  80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  221 VAL
Chi-restraints excluded: chain C residue  232 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 37 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0000
   chunk 19 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.1790

-------------------------------------------------------------------------------
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 = 0.4204 r_free = 0.4204 target = 0.149336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.128076 restraints weight = 3877.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3987 rms_B_bonded: 2.85
r_work: 0.3863 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3313  Z= 0.109
  Angle     :  0.556   6.034   4505  Z= 0.303
  Chirality :  0.051   0.170    543
  Planarity :  0.002   0.008    558
  Dihedral  :  5.937  21.691    447
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.49 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.03 (0.32), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.82 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS B 239 
 PHE   0.007   0.001   PHE B 237 
 TYR   0.020   0.001   TYR C 236 
 ARG   0.001   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01648 (   22)
  hydrogen bonds       : angle       5.65931 (   66)
  SS BOND              : bond        0.00257 (    1)
  SS BOND              : angle       0.23128 (    2)
  covalent geometry    : bond        0.00246 ( 3312)
  covalent geometry    : angle       0.55611 ( 4503)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.361 
Fit side-chains
REVERT: B  146 ILE cc_start: 0.8994 (pt) cc_final: 0.8722 (pt)
REVERT: A  210 MET cc_start: 0.8515 (mtm) cc_final: 0.8162 (mtp)
REVERT: C  220 LYS cc_start: 0.9161 (mttt) cc_final: 0.8759 (mttm)
  outliers start: 9
  outliers final: 5
  residues processed: 85
  average time/residue: 0.1501
  time to fit residues: 15.4727
Evaluate side-chains
  81 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain C residue  232 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 2 optimal weight:    0.0870
   chunk 36 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 9 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   chunk 12 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    2.8166

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

Flipped N/Q/H residues before XYZ refinement:
B 223 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.141642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.120791 restraints weight = 4129.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3906 rms_B_bonded: 2.96
r_work: 0.3791 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3313  Z= 0.205
  Angle     :  0.648   5.946   4505  Z= 0.355
  Chirality :  0.052   0.170    543
  Planarity :  0.002   0.010    558
  Dihedral  :  6.282  20.893    447
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 16.40 %
    Favored  : 80.95 %
  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: -4.97 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.78 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS B 239 
 PHE   0.010   0.002   PHE B 237 
 TYR   0.025   0.002   TYR C 236 
 ARG   0.001   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02466 (   22)
  hydrogen bonds       : angle       5.75065 (   66)
  SS BOND              : bond        0.00447 (    1)
  SS BOND              : angle       0.49425 (    2)
  covalent geometry    : bond        0.00476 ( 3312)
  covalent geometry    : angle       0.64757 ( 4503)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.334 
Fit side-chains
REVERT: B  146 ILE cc_start: 0.9093 (pt) cc_final: 0.8838 (pt)
REVERT: B  210 MET cc_start: 0.8698 (mtt) cc_final: 0.8357 (mtp)
REVERT: A  210 MET cc_start: 0.8434 (mtm) cc_final: 0.8046 (mtp)
REVERT: C  220 LYS cc_start: 0.9115 (mttt) cc_final: 0.8711 (mttm)
  outliers start: 10
  outliers final: 7
  residues processed: 75
  average time/residue: 0.1724
  time to fit residues: 15.5133
Evaluate side-chains
  74 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  232 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 26 optimal weight:    0.0670
   chunk 21 optimal weight:   10.0000
   chunk 15 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 27 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 34 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0050
   overall best weight:    0.7934

-------------------------------------------------------------------------------
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 = 0.4278 r_free = 0.4278 target = 0.155628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.133437 restraints weight = 3880.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.4052 rms_B_bonded: 3.09
r_work: 0.3907 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.2949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3313  Z= 0.097
  Angle     :  0.568   5.910   4505  Z= 0.309
  Chirality :  0.052   0.167    543
  Planarity :  0.002   0.010    558
  Dihedral  :  5.823  21.839    447
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.93 %
    Favored  : 80.95 %
  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: -4.87 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.70 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS B 239 
 PHE   0.006   0.001   PHE B 237 
 TYR   0.025   0.001   TYR C 236 
 ARG   0.001   0.000   ARG A 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01479 (   22)
  hydrogen bonds       : angle       5.64402 (   66)
  SS BOND              : bond        0.00220 (    1)
  SS BOND              : angle       0.24900 (    2)
  covalent geometry    : bond        0.00215 ( 3312)
  covalent geometry    : angle       0.56827 ( 4503)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: B  146 ILE cc_start: 0.9073 (pt) cc_final: 0.8818 (pt)
REVERT: B  210 MET cc_start: 0.8651 (mtt) cc_final: 0.8360 (mtp)
REVERT: A  210 MET cc_start: 0.8398 (mtm) cc_final: 0.8045 (mtp)
REVERT: C  128 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8258 (t)
REVERT: C  220 LYS cc_start: 0.9114 (mttt) cc_final: 0.8771 (mttm)
  outliers start: 8
  outliers final: 6
  residues processed: 77
  average time/residue: 0.1532
  time to fit residues: 14.1907
Evaluate side-chains
  77 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  232 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 24 optimal weight:    6.9990
   chunk 4 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 35 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.4177 r_free = 0.4177 target = 0.145482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.124515 restraints weight = 4008.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3966 rms_B_bonded: 2.93
r_work: 0.3847 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3720 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.2875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3313  Z= 0.155
  Angle     :  0.609   6.260   4505  Z= 0.333
  Chirality :  0.051   0.166    543
  Planarity :  0.002   0.009    558
  Dihedral  :  5.930  21.029    447
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 16.93 %
    Favored  : 79.89 %
  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: -4.84 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.68 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B 239 
 PHE   0.010   0.001   PHE B 237 
 TYR   0.022   0.002   TYR B 197 
 ARG   0.001   0.000   ARG C 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01926 (   22)
  hydrogen bonds       : angle       5.61655 (   66)
  SS BOND              : bond        0.00332 (    1)
  SS BOND              : angle       0.43163 (    2)
  covalent geometry    : bond        0.00364 ( 3312)
  covalent geometry    : angle       0.60947 ( 4503)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: B  129 LYS cc_start: 0.8904 (ptmt) cc_final: 0.8514 (pttt)
REVERT: B  146 ILE cc_start: 0.9083 (pt) cc_final: 0.8802 (pt)
REVERT: B  210 MET cc_start: 0.8816 (mtt) cc_final: 0.8556 (mtp)
REVERT: A  171 PHE cc_start: 0.9387 (m-80) cc_final: 0.9108 (m-80)
REVERT: A  207 MET cc_start: 0.8335 (mtm) cc_final: 0.8121 (mtm)
REVERT: A  210 MET cc_start: 0.8506 (mtm) cc_final: 0.8164 (mtp)
REVERT: A  236 TYR cc_start: 0.9058 (t80) cc_final: 0.8831 (t80)
REVERT: C  220 LYS cc_start: 0.9148 (mttt) cc_final: 0.8750 (mttm)
  outliers start: 12
  outliers final: 9
  residues processed: 77
  average time/residue: 0.1773
  time to fit residues: 16.2623
Evaluate side-chains
  79 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain C residue  207 MET
Chi-restraints excluded: chain C residue  217 ILE
Chi-restraints excluded: chain C residue  232 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 9 optimal weight:    8.9990
   chunk 15 optimal weight:    8.9990
   chunk 28 optimal weight:    2.9990
   chunk 6 optimal weight:    8.9990
   chunk 38 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   chunk 34 optimal weight:    0.1980
   chunk 37 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.4265 r_free = 0.4265 target = 0.152782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.131645 restraints weight = 3872.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.4082 rms_B_bonded: 2.97
r_work: 0.3975 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3847 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.3246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3313  Z= 0.099
  Angle     :  0.566   6.037   4505  Z= 0.308
  Chirality :  0.051   0.166    543
  Planarity :  0.002   0.009    558
  Dihedral  :  5.637  22.194    447
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 17.20 %
    Favored  : 80.16 %
  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: -4.75 (0.32), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.61 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS B 239 
 PHE   0.006   0.001   PHE B 237 
 TYR   0.023   0.002   TYR C 236 
 ARG   0.001   0.000   ARG A 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01385 (   22)
  hydrogen bonds       : angle       5.53022 (   66)
  SS BOND              : bond        0.00213 (    1)
  SS BOND              : angle       0.27122 (    2)
  covalent geometry    : bond        0.00224 ( 3312)
  covalent geometry    : angle       0.56606 ( 4503)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
REVERT: B  129 LYS cc_start: 0.9025 (ptmt) cc_final: 0.8821 (pttt)
REVERT: B  146 ILE cc_start: 0.9046 (pt) cc_final: 0.8739 (pt)
REVERT: B  210 MET cc_start: 0.8804 (mtt) cc_final: 0.8571 (mtp)
REVERT: A  171 PHE cc_start: 0.9316 (m-80) cc_final: 0.9098 (m-80)
REVERT: A  210 MET cc_start: 0.8542 (mtm) cc_final: 0.8308 (mtp)
REVERT: C  128 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8374 (t)
REVERT: C  220 LYS cc_start: 0.9213 (mttt) cc_final: 0.8832 (mttm)
  outliers start: 10
  outliers final: 6
  residues processed: 74
  average time/residue: 0.1593
  time to fit residues: 14.3130
Evaluate side-chains
  75 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  217 ILE
Chi-restraints excluded: chain C residue  232 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 16 optimal weight:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    1.9986

-------------------------------------------------------------------------------
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 = 0.4179 r_free = 0.4179 target = 0.145285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.124167 restraints weight = 4045.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3982 rms_B_bonded: 2.95
r_work: 0.3855 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3313  Z= 0.155
  Angle     :  0.624   6.499   4505  Z= 0.339
  Chirality :  0.051   0.166    543
  Planarity :  0.002   0.008    558
  Dihedral  :  5.864  20.987    447
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.02 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 17.72 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.79 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.64 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS B 239 
 PHE   0.010   0.001   PHE A 237 
 TYR   0.020   0.002   TYR C 236 
 ARG   0.001   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01884 (   22)
  hydrogen bonds       : angle       5.57248 (   66)
  SS BOND              : bond        0.00327 (    1)
  SS BOND              : angle       0.40154 (    2)
  covalent geometry    : bond        0.00363 ( 3312)
  covalent geometry    : angle       0.62378 ( 4503)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: B  129 LYS cc_start: 0.8904 (ptmt) cc_final: 0.8554 (pttt)
REVERT: B  146 ILE cc_start: 0.9067 (pt) cc_final: 0.8778 (pt)
REVERT: B  209 TYR cc_start: 0.8062 (m-80) cc_final: 0.7807 (m-80)
REVERT: B  210 MET cc_start: 0.8686 (mtt) cc_final: 0.8418 (mtp)
REVERT: A  171 PHE cc_start: 0.9278 (m-80) cc_final: 0.9024 (m-80)
REVERT: A  210 MET cc_start: 0.8361 (mtm) cc_final: 0.8031 (mtp)
REVERT: C  220 LYS cc_start: 0.9135 (mttt) cc_final: 0.8724 (mttm)
  outliers start: 11
  outliers final: 10
  residues processed: 75
  average time/residue: 0.1731
  time to fit residues: 15.4321
Evaluate side-chains
  80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  207 MET
Chi-restraints excluded: chain C residue  217 ILE
Chi-restraints excluded: chain C residue  232 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 21 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    9.9990
   chunk 3 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 27 optimal weight:    8.9990
   chunk 11 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 15 optimal weight:    7.9990
   overall best weight:    2.5386

-------------------------------------------------------------------------------
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 = 0.4162 r_free = 0.4162 target = 0.144216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.123367 restraints weight = 4002.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3952 rms_B_bonded: 2.93
r_work: 0.3827 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3313  Z= 0.188
  Angle     :  0.644   6.072   4505  Z= 0.351
  Chirality :  0.052   0.169    543
  Planarity :  0.002   0.017    558
  Dihedral  :  6.067  21.383    447
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.02 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.99 %
    Favored  : 78.84 %
  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: -4.81 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.66 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS B 239 
 PHE   0.011   0.001   PHE A 237 
 TYR   0.025   0.002   TYR A 236 
 ARG   0.001   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02118 (   22)
  hydrogen bonds       : angle       5.60318 (   66)
  SS BOND              : bond        0.00382 (    1)
  SS BOND              : angle       0.56415 (    2)
  covalent geometry    : bond        0.00439 ( 3312)
  covalent geometry    : angle       0.64371 ( 4503)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: B  129 LYS cc_start: 0.8874 (ptmt) cc_final: 0.8487 (pttt)
REVERT: B  146 ILE cc_start: 0.9087 (pt) cc_final: 0.8799 (pt)
REVERT: B  209 TYR cc_start: 0.8095 (m-80) cc_final: 0.7846 (m-80)
REVERT: B  210 MET cc_start: 0.8719 (mtt) cc_final: 0.8447 (mtp)
REVERT: A  210 MET cc_start: 0.8366 (mtm) cc_final: 0.8040 (mtp)
REVERT: C  220 LYS cc_start: 0.9138 (mttt) cc_final: 0.8779 (mttm)
  outliers start: 12
  outliers final: 10
  residues processed: 74
  average time/residue: 0.1806
  time to fit residues: 15.7919
Evaluate side-chains
  78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  180 ARG
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  207 MET
Chi-restraints excluded: chain C residue  217 ILE
Chi-restraints excluded: chain C residue  232 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 0 optimal weight:    0.9980
   chunk 30 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 7 optimal weight:    0.2980
   chunk 35 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9990
   chunk 19 optimal weight:    8.9990
   overall best weight:    1.4586

-------------------------------------------------------------------------------
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 = 0.4229 r_free = 0.4229 target = 0.148945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.127535 restraints weight = 4004.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.4035 rms_B_bonded: 2.99
r_work: 0.3903 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.3121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3313  Z= 0.127
  Angle     :  0.606   5.952   4505  Z= 0.329
  Chirality :  0.052   0.167    543
  Planarity :  0.002   0.015    558
  Dihedral  :  5.857  22.120    447
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 18.78 %
    Favored  : 79.10 %
  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: -4.76 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.62 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS B 239 
 PHE   0.008   0.001   PHE A 237 
 TYR   0.027   0.002   TYR A 236 
 ARG   0.001   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01639 (   22)
  hydrogen bonds       : angle       5.63390 (   66)
  SS BOND              : bond        0.00267 (    1)
  SS BOND              : angle       0.41137 (    2)
  covalent geometry    : bond        0.00295 ( 3312)
  covalent geometry    : angle       0.60577 ( 4503)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1912.11 seconds
wall clock time: 33 minutes 36.12 seconds (2016.12 seconds total)