Starting phenix.real_space_refine
on Fri Aug 22 13:23:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j7p_36045/08_2025/8j7p_36045.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j7p_36045/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j7p_36045/08_2025/8j7p_36045.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j7p_36045/08_2025/8j7p_36045.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j7p_36045/08_2025/8j7p_36045.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j7p_36045/08_2025/8j7p_36045.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3258
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      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:
    A, C
  Time building chain proxies: 0.77, per 1000 atoms: 0.24
  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=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 253 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 253 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.21
  Conformation dependent library (CDL) restraints added in 127.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.17
  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: 0.40

  Time building geometry restraints manager: 0.28 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: 1752
       14.06 -    28.11: 195
       28.11 -    42.17: 36
       42.17 -    56.22: 9
       56.22 -    70.28: 3
  Dihedral angle restraints: 1995
    sinusoidal: 777
      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 1992 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:
        2.40 -     2.90: 1410
        2.90 -     3.40: 2835
        3.40 -     3.90: 5193
        3.90 -     4.40: 5689
        4.40 -     4.90: 11123
  Nonbonded interactions: 26250
  Sorted by model distance:
  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
  nonbonded pdb=" OG1 THR C 233 "
            pdb=" N   THR C 234 "
     model   vdw
     2.405 3.120
  nonbonded pdb=" OG1 THR B 233 "
            pdb=" N   THR B 234 "
     model   vdw
     2.405 3.120
  ... (remaining 26245 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
  selection = chain 'C'
}

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:             2.150
  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:             0.020
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.490
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.890
-------------------------------------------------------------------------------
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   3315  Z= 0.419
  Angle     :  0.807   5.994   4509  Z= 0.458
  Chirality :  0.056   0.175    543
  Planarity :  0.003   0.011    558
  Dihedral  : 12.537  70.278   1206
  Min Nonbonded Distance : 2.402

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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.002   0.000   ARG A 247 
 TYR   0.023   0.003   TYR C 143 
 PHE   0.010   0.003   PHE C 237 
 HIS   0.005   0.003   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00926 ( 3312)
  covalent geometry    : angle       0.80697 ( 4503)
  SS BOND              : bond        0.00587 (    3)
  SS BOND              : angle       0.88596 (    6)
  hydrogen bonds       : bond        0.18382 (   22)
  hydrogen bonds       : angle       9.09638 (   66)

*********************** 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  : 0.126 
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: 0.0832
  time to fit residues: 7.6587
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  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    0.0980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.6186

-------------------------------------------------------------------------------
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 = 0.4107 r_free = 0.4107 target = 0.143616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.122461 restraints weight = 3968.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3910 rms_B_bonded: 2.87
r_work: 0.3801 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3673 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3315  Z= 0.139
  Angle     :  0.610   6.449   4509  Z= 0.328
  Chirality :  0.053   0.175    543
  Planarity :  0.002   0.008    558
  Dihedral  :  6.341  20.056    447
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 12.70 %
    Favored  : 85.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.41 (0.30), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.11 (0.23), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 140 
 TYR   0.014   0.002   TYR A 143 
 PHE   0.008   0.001   PHE B 237 
 HIS   0.005   0.002   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 3312)
  covalent geometry    : angle       0.61067 ( 4503)
  SS BOND              : bond        0.00276 (    3)
  SS BOND              : angle       0.23091 (    6)
  hydrogen bonds       : bond        0.02572 (   22)
  hydrogen bonds       : angle       6.21649 (   66)

*********************** 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
  97 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.145 
Fit side-chains
REVERT: B  146 ILE cc_start: 0.8907 (pt) cc_final: 0.8666 (pt)
REVERT: B  210 MET cc_start: 0.8872 (mtt) cc_final: 0.8638 (mtm)
REVERT: A  146 ILE cc_start: 0.8879 (pt) cc_final: 0.8664 (pt)
REVERT: A  207 MET cc_start: 0.8468 (mtm) cc_final: 0.8162 (mtm)
REVERT: C  210 MET cc_start: 0.8439 (mtt) cc_final: 0.8123 (mtp)
REVERT: C  220 LYS cc_start: 0.9209 (mttt) cc_final: 0.8870 (mttm)
  outliers start: 5
  outliers final: 4
  residues processed: 92
  average time/residue: 0.0652
  time to fit residues: 7.2744
Evaluate side-chains
  81 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain C residue  175 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 20 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0980
   chunk 36 optimal weight:    0.7980
   chunk 9 optimal weight:    7.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.4180 r_free = 0.4180 target = 0.148386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.126789 restraints weight = 3834.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3960 rms_B_bonded: 2.87
r_work: 0.3837 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3715 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3315  Z= 0.109
  Angle     :  0.584   5.882   4509  Z= 0.317
  Chirality :  0.052   0.168    543
  Planarity :  0.002   0.009    558
  Dihedral  :  5.941  22.443    447
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.81 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.16 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.93 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 140 
 TYR   0.022   0.001   TYR C 236 
 PHE   0.007   0.001   PHE B 237 
 HIS   0.005   0.002   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 3312)
  covalent geometry    : angle       0.58405 ( 4503)
  SS BOND              : bond        0.00240 (    3)
  SS BOND              : angle       0.25527 (    6)
  hydrogen bonds       : bond        0.01881 (   22)
  hydrogen bonds       : angle       5.73445 (   66)

*********************** 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
  96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.100 
Fit side-chains
REVERT: B  146 ILE cc_start: 0.8897 (pt) cc_final: 0.8594 (pt)
REVERT: B  170 GLN cc_start: 0.9136 (mp10) cc_final: 0.8851 (mp10)
REVERT: B  207 MET cc_start: 0.8206 (mtm) cc_final: 0.7684 (mtm)
REVERT: A  146 ILE cc_start: 0.8976 (pt) cc_final: 0.8725 (pt)
REVERT: A  207 MET cc_start: 0.8233 (mtm) cc_final: 0.7836 (mpp)
REVERT: A  210 MET cc_start: 0.8563 (mtm) cc_final: 0.8297 (mtp)
REVERT: C  210 MET cc_start: 0.8374 (mtt) cc_final: 0.8134 (mtp)
REVERT: C  220 LYS cc_start: 0.9167 (mttt) cc_final: 0.8793 (mttm)
  outliers start: 9
  outliers final: 7
  residues processed: 89
  average time/residue: 0.0724
  time to fit residues: 7.7210
Evaluate side-chains
  87 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
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  207 MET
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 22 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0270
   chunk 27 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 2 optimal weight:    8.9990
   chunk 33 optimal weight:    0.6980
   chunk 10 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 34 optimal weight:    9.9990
   overall best weight:    2.3242

-------------------------------------------------------------------------------
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 = 0.4104 r_free = 0.4104 target = 0.141683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.120292 restraints weight = 3970.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3907 rms_B_bonded: 2.86
r_work: 0.3797 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3672 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3315  Z= 0.174
  Angle     :  0.611   5.850   4509  Z= 0.336
  Chirality :  0.052   0.169    543
  Planarity :  0.002   0.007    558
  Dihedral  :  6.100  19.260    447
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 15.34 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.04 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.83 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 140 
 TYR   0.015   0.002   TYR A 209 
 PHE   0.009   0.001   PHE B 237 
 HIS   0.005   0.002   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 3312)
  covalent geometry    : angle       0.61160 ( 4503)
  SS BOND              : bond        0.00318 (    3)
  SS BOND              : angle       0.42705 (    6)
  hydrogen bonds       : bond        0.02343 (   22)
  hydrogen bonds       : angle       5.75672 (   66)

*********************** 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
  86 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.125 
Fit side-chains
REVERT: B  146 ILE cc_start: 0.9039 (pt) cc_final: 0.8754 (pt)
REVERT: B  170 GLN cc_start: 0.9177 (mp10) cc_final: 0.8908 (mp10)
REVERT: B  210 MET cc_start: 0.8617 (mtm) cc_final: 0.8305 (mtp)
REVERT: A  146 ILE cc_start: 0.9009 (pt) cc_final: 0.8694 (pt)
REVERT: A  210 MET cc_start: 0.8527 (mtm) cc_final: 0.8290 (mtp)
REVERT: C  210 MET cc_start: 0.8397 (mtt) cc_final: 0.8168 (mtp)
REVERT: C  220 LYS cc_start: 0.9193 (mttt) cc_final: 0.8819 (mttm)
  outliers start: 11
  outliers final: 9
  residues processed: 78
  average time/residue: 0.0672
  time to fit residues: 6.3595
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  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 LEU
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  207 MET
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 22 optimal weight:    9.9990
   chunk 5 optimal weight:    0.0770
   chunk 17 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 9 optimal weight:    9.9990
   chunk 24 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.9342

-------------------------------------------------------------------------------
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 = 0.4228 r_free = 0.4228 target = 0.152489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.130229 restraints weight = 3785.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.4006 rms_B_bonded: 3.05
r_work: 0.3883 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3315  Z= 0.101
  Angle     :  0.568   5.893   4509  Z= 0.311
  Chirality :  0.051   0.164    543
  Planarity :  0.002   0.007    558
  Dihedral  :  5.779  19.852    447
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 17.20 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.93 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.75 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 140 
 TYR   0.016   0.001   TYR A 236 
 PHE   0.006   0.001   PHE B 237 
 HIS   0.004   0.002   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 3312)
  covalent geometry    : angle       0.56800 ( 4503)
  SS BOND              : bond        0.00214 (    3)
  SS BOND              : angle       0.23691 (    6)
  hydrogen bonds       : bond        0.01579 (   22)
  hydrogen bonds       : angle       5.62300 (   66)

*********************** 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
  85 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.123 
Fit side-chains
REVERT: B  146 ILE cc_start: 0.9001 (pt) cc_final: 0.8712 (pt)
REVERT: B  210 MET cc_start: 0.8686 (mtt) cc_final: 0.8349 (mtp)
REVERT: A  146 ILE cc_start: 0.8962 (pt) cc_final: 0.8627 (pt)
REVERT: A  210 MET cc_start: 0.8411 (mtm) cc_final: 0.8163 (mtp)
REVERT: C  207 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.7014 (mmm)
REVERT: C  210 MET cc_start: 0.8313 (mtt) cc_final: 0.8077 (mtp)
REVERT: C  220 LYS cc_start: 0.9120 (mttt) cc_final: 0.8752 (mttm)
  outliers start: 9
  outliers final: 7
  residues processed: 77
  average time/residue: 0.0636
  time to fit residues: 5.8245
Evaluate side-chains
  80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
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  207 MET
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 17 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 8 optimal weight:    0.0370
   chunk 16 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   overall best weight:    2.2066

-------------------------------------------------------------------------------
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 = 0.4169 r_free = 0.4169 target = 0.146236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.124103 restraints weight = 3867.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 3.04
r_work: 0.3807 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3315  Z= 0.166
  Angle     :  0.599   5.795   4509  Z= 0.329
  Chirality :  0.052   0.165    543
  Planarity :  0.002   0.015    558
  Dihedral  :  5.971  18.986    447
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 17.46 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.89 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.72 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 140 
 TYR   0.016   0.002   TYR A 209 
 PHE   0.009   0.002   PHE B 237 
 HIS   0.005   0.002   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 3312)
  covalent geometry    : angle       0.59898 ( 4503)
  SS BOND              : bond        0.00275 (    3)
  SS BOND              : angle       0.42243 (    6)
  hydrogen bonds       : bond        0.02141 (   22)
  hydrogen bonds       : angle       5.63762 (   66)

*********************** 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: 11
    poor density    : 73
  time to evaluate  : 0.131 
Fit side-chains
REVERT: B  146 ILE cc_start: 0.9052 (pt) cc_final: 0.8756 (pt)
REVERT: B  210 MET cc_start: 0.8675 (mtt) cc_final: 0.8412 (mtp)
REVERT: A  146 ILE cc_start: 0.8917 (pt) cc_final: 0.8604 (pt)
REVERT: A  210 MET cc_start: 0.8441 (mtm) cc_final: 0.8106 (mtp)
REVERT: C  210 MET cc_start: 0.8356 (mtt) cc_final: 0.8102 (mtp)
REVERT: C  220 LYS cc_start: 0.9143 (mttt) cc_final: 0.8754 (mttm)
  outliers start: 11
  outliers final: 8
  residues processed: 77
  average time/residue: 0.0653
  time to fit residues: 6.0636
Evaluate side-chains
  75 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
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  160 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 34 optimal weight:    0.8980
   chunk 22 optimal weight:   10.0000
   chunk 10 optimal weight:    5.9990
   chunk 14 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 1 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
B 183 ASN
A 222 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.139795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.118239 restraints weight = 4086.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3845 rms_B_bonded: 3.04
r_work: 0.3706 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.037   3315  Z= 0.290
  Angle     :  0.688   6.799   4509  Z= 0.382
  Chirality :  0.053   0.177    543
  Planarity :  0.002   0.013    558
  Dihedral  :  6.450  21.608    447
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.53 %
    Favored  : 88.47 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.20 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.97 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.78 (0.23), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 180 
 TYR   0.019   0.003   TYR B 143 
 PHE   0.012   0.002   PHE B 237 
 HIS   0.005   0.003   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00674 ( 3312)
  covalent geometry    : angle       0.68781 ( 4503)
  SS BOND              : bond        0.00457 (    3)
  SS BOND              : angle       0.65346 (    6)
  hydrogen bonds       : bond        0.02764 (   22)
  hydrogen bonds       : angle       5.74071 (   66)

*********************** 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
  81 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.134 
Fit side-chains
REVERT: B  146 ILE cc_start: 0.9066 (pt) cc_final: 0.8784 (pt)
REVERT: B  210 MET cc_start: 0.8752 (mtt) cc_final: 0.8474 (mtp)
REVERT: A  146 ILE cc_start: 0.8941 (pt) cc_final: 0.8649 (pt)
REVERT: A  171 PHE cc_start: 0.9355 (m-80) cc_final: 0.9120 (m-80)
REVERT: A  207 MET cc_start: 0.8378 (mtm) cc_final: 0.8080 (mtm)
REVERT: A  210 MET cc_start: 0.8400 (mtm) cc_final: 0.8047 (mtp)
REVERT: A  235 THR cc_start: 0.8518 (m) cc_final: 0.8093 (p)
REVERT: C  210 MET cc_start: 0.8341 (mtt) cc_final: 0.8080 (mtp)
REVERT: C  220 LYS cc_start: 0.9141 (mttt) cc_final: 0.8791 (mttm)
  outliers start: 12
  outliers final: 9
  residues processed: 75
  average time/residue: 0.0786
  time to fit residues: 6.9462
Evaluate side-chains
  77 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
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  160 VAL
Chi-restraints excluded: chain C residue  221 VAL
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 32 optimal weight:    7.9990
   chunk 21 optimal weight:    7.9990
   chunk 11 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   overall best weight:    1.7784

-------------------------------------------------------------------------------
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 = 0.4173 r_free = 0.4173 target = 0.147291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.125261 restraints weight = 4012.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 3.06
r_work: 0.3823 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3315  Z= 0.141
  Angle     :  0.599   6.292   4509  Z= 0.329
  Chirality :  0.052   0.167    543
  Planarity :  0.002   0.012    558
  Dihedral  :  6.045  20.500    447
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 17.99 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.87 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.71 (0.23), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 140 
 TYR   0.026   0.002   TYR A 236 
 PHE   0.008   0.001   PHE B 237 
 HIS   0.004   0.002   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 3312)
  covalent geometry    : angle       0.59900 ( 4503)
  SS BOND              : bond        0.00266 (    3)
  SS BOND              : angle       0.29122 (    6)
  hydrogen bonds       : bond        0.01790 (   22)
  hydrogen bonds       : angle       5.67225 (   66)

*********************** 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  : 0.193 
Fit side-chains
REVERT: B  146 ILE cc_start: 0.9043 (pt) cc_final: 0.8747 (pt)
REVERT: B  210 MET cc_start: 0.8757 (mtt) cc_final: 0.8468 (mtp)
REVERT: A  146 ILE cc_start: 0.8942 (pt) cc_final: 0.8632 (pt)
REVERT: A  210 MET cc_start: 0.8364 (mtm) cc_final: 0.8047 (mtp)
REVERT: C  210 MET cc_start: 0.8293 (mtt) cc_final: 0.8067 (mtp)
REVERT: C  220 LYS cc_start: 0.9158 (mttt) cc_final: 0.8812 (mttm)
  outliers start: 10
  outliers final: 8
  residues processed: 78
  average time/residue: 0.0767
  time to fit residues: 7.1696
Evaluate side-chains
  76 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  180 ARG
Chi-restraints excluded: chain B residue  216 LEU
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  232 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 30 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0270
   chunk 38 optimal weight:    0.9980
   chunk 35 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 34 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0470
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.5938

-------------------------------------------------------------------------------
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 = 0.4309 r_free = 0.4309 target = 0.158955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.136469 restraints weight = 3806.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.4080 rms_B_bonded: 3.05
r_work: 0.3940 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.3268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3315  Z= 0.092
  Angle     :  0.570   6.443   4509  Z= 0.308
  Chirality :  0.051   0.165    543
  Planarity :  0.002   0.011    558
  Dihedral  :  5.538  19.938    447
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 19.58 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.001   0.000   ARG C 247 
 TYR   0.025   0.001   TYR A 236 
 PHE   0.006   0.001   PHE A 237 
 HIS   0.004   0.002   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 ( 3312)
  covalent geometry    : angle       0.56987 ( 4503)
  SS BOND              : bond        0.00163 (    3)
  SS BOND              : angle       0.15778 (    6)
  hydrogen bonds       : bond        0.01334 (   22)
  hydrogen bonds       : angle       5.65501 (   66)

*********************** 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
  80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: B  210 MET cc_start: 0.8660 (mtt) cc_final: 0.8389 (mtp)
REVERT: A  146 ILE cc_start: 0.8940 (pt) cc_final: 0.8653 (pt)
REVERT: A  210 MET cc_start: 0.8334 (mtm) cc_final: 0.8054 (mtp)
REVERT: C  128 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8263 (t)
REVERT: C  220 LYS cc_start: 0.9150 (mttt) cc_final: 0.8802 (mttm)
  outliers start: 7
  outliers final: 4
  residues processed: 76
  average time/residue: 0.0801
  time to fit residues: 7.2687
Evaluate side-chains
  72 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 9 optimal weight:    7.9990
   chunk 8 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 13 optimal weight:    9.9990
   chunk 7 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 0 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   overall best weight:    1.1586

-------------------------------------------------------------------------------
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 = 0.4233 r_free = 0.4233 target = 0.151078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.129081 restraints weight = 4012.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.4040 rms_B_bonded: 3.05
r_work: 0.3910 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.3209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3315  Z= 0.109
  Angle     :  0.566   6.192   4509  Z= 0.308
  Chirality :  0.051   0.169    543
  Planarity :  0.002   0.010    558
  Dihedral  :  5.481  17.976    447
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 19.05 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.67 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.55 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 247 
 TYR   0.024   0.001   TYR A 236 
 PHE   0.007   0.001   PHE A 237 
 HIS   0.004   0.002   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 3312)
  covalent geometry    : angle       0.56597 ( 4503)
  SS BOND              : bond        0.00184 (    3)
  SS BOND              : angle       0.24013 (    6)
  hydrogen bonds       : bond        0.01406 (   22)
  hydrogen bonds       : angle       5.62340 (   66)

********************** 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
  78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.145 
Fit side-chains
REVERT: B  146 ILE cc_start: 0.9051 (pt) cc_final: 0.8733 (pt)
REVERT: B  210 MET cc_start: 0.8686 (mtt) cc_final: 0.8418 (mtp)
REVERT: A  146 ILE cc_start: 0.8944 (pt) cc_final: 0.8608 (pt)
REVERT: A  210 MET cc_start: 0.8339 (mtm) cc_final: 0.8060 (mtp)
REVERT: C  220 LYS cc_start: 0.9141 (mttt) cc_final: 0.8789 (mttm)
  outliers start: 6
  outliers final: 6
  residues processed: 72
  average time/residue: 0.0780
  time to fit residues: 6.7737
Evaluate side-chains
  77 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
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  232 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   chunk 22 optimal weight:    8.9990
   chunk 11 optimal weight:    4.9990
   chunk 34 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 4 optimal weight:    6.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 = 0.4231 r_free = 0.4231 target = 0.150334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.128202 restraints weight = 4032.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.4026 rms_B_bonded: 3.02
r_work: 0.3897 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.3234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3315  Z= 0.120
  Angle     :  0.588   6.601   4509  Z= 0.317
  Chirality :  0.051   0.169    543
  Planarity :  0.002   0.010    558
  Dihedral  :  5.547  18.601    447
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.58 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.63 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.52 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 247 
 TYR   0.023   0.002   TYR A 236 
 PHE   0.007   0.001   PHE B 237 
 HIS   0.004   0.002   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 3312)
  covalent geometry    : angle       0.58794 ( 4503)
  SS BOND              : bond        0.00203 (    3)
  SS BOND              : angle       0.27635 (    6)
  hydrogen bonds       : bond        0.01567 (   22)
  hydrogen bonds       : angle       5.60117 (   66)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 927.92 seconds
wall clock time: 16 minutes 32.59 seconds (992.59 seconds total)