Starting phenix.real_space_refine
on Fri Oct 10 10:52:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x5h_38069/10_2025/8x5h_38069.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x5h_38069/10_2025/8x5h_38069.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x5h_38069/10_2025/8x5h_38069.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x5h_38069/10_2025/8x5h_38069.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x5h_38069/10_2025/8x5h_38069.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x5h_38069/10_2025/8x5h_38069.map"
  }
  resolution = 3.47
  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-2.0-5842/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: 0.76, per 1000 atoms: 0.23
  Number of scatterers: 3258
  At special positions: 0
  Unit cell: (100.43, 97.94, 34.86, 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=2.02
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 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: 0.15
  Conformation dependent library (CDL) restraints added in 77.8 milliseconds
  
  Enol-peptide restraints added in 238.4 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 12 sheets defined
      0.0% alpha, 30.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 130
      removed outlier: 6.664A  pdb=" N   LYS B 129 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 137
      removed outlier: 6.589A  pdb=" N   SER B 134 " --> pdb=" O   TYR C 135 " (cutoff:3.500A)
      removed outlier: 8.219A  pdb=" N   VAL C 137 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   ASP B 136 " --> pdb=" O   VAL C 137 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 144
      removed outlier: 6.536A  pdb=" N   ILE B 142 " --> pdb=" O   TYR C 143 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 156
      removed outlier: 6.564A  pdb=" N   ASN B 155 " --> pdb=" O   ASN C 156 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 164
      removed outlier: 6.985A  pdb=" N   GLU B 163 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 167 through 169
      removed outlier: 6.555A  pdb=" N   GLN B 168 " --> pdb=" O   VAL C 169 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 185 through 187
      removed outlier: 6.495A  pdb=" N   THR B 185 " --> pdb=" O   ILE A 186 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 190 through 192
      removed outlier: 6.466A  pdb=" N   ASP B 191 " --> pdb=" O   MET C 192 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 201 through 213
      removed outlier: 8.949A  pdb=" N   VAL B 202 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 9.868A  pdb=" N   GLU A 205 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   ALA B 204 " --> pdb=" O   GLU A 205 " (cutoff:3.500A)
      removed outlier: 8.194A  pdb=" N   MET A 207 " --> pdb=" O   ALA B 204 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   GLU B 206 " --> pdb=" O   MET A 207 " (cutoff:3.500A)
      removed outlier: 8.258A  pdb=" N   TYR A 209 " --> pdb=" O   GLU B 206 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   SER B 208 " --> pdb=" O   TYR A 209 " (cutoff:3.500A)
      removed outlier: 8.100A  pdb=" N   TYR A 211 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   MET B 210 " --> pdb=" O   TYR A 211 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   PHE A 213 " --> pdb=" O   MET B 210 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   ASP B 212 " --> pdb=" O   PHE A 213 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   VAL C 202 " --> pdb=" O   THR B 201 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   ILE B 203 " --> pdb=" O   VAL C 202 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ALA C 204 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 222 through 230
      removed outlier: 7.012A  pdb=" N   VAL B 230 " --> pdb=" O   GLN A 229 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   ASN B 223 " --> pdb=" O   ILE C 224 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   LEU C 226 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   VAL B 225 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   MET C 228 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   MET B 227 " --> pdb=" O   MET C 228 " (cutoff:3.500A)
      removed outlier: 7.458A  pdb=" N   VAL C 230 " --> pdb=" O   MET B 227 " (cutoff:3.500A)
      removed outlier: 8.215A  pdb=" N   GLN B 229 " --> pdb=" O   VAL C 230 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 242 through 244
      removed outlier: 6.310A  pdb=" N   GLN B 242 " --> pdb=" O   ILE C 243 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 251 through 253
      removed outlier: 6.434A  pdb=" N   ASP B 252 " --> pdb=" O   CYS A 253 " (cutoff:3.500A)

    36 hydrogen bonds defined for protein.
    108 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: 0.34

  Time building geometry restraints manager: 0.22 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1017
        1.33 -     1.45: 426
        1.45 -     1.57: 1833
        1.57 -     1.68: 0
        1.68 -     1.80: 36
  Bond restraints: 3312
  Sorted by residual:
  bond pdb=" CG  LEU A 144 "
       pdb=" CD2 LEU A 144 "
    ideal  model  delta    sigma   weight residual
    1.521  1.471  0.050 3.30e-02 9.18e+02 2.27e+00
  bond pdb=" CG  LEU B 144 "
       pdb=" CD2 LEU B 144 "
    ideal  model  delta    sigma   weight residual
    1.521  1.471  0.050 3.30e-02 9.18e+02 2.26e+00
  bond pdb=" CG  LEU C 144 "
       pdb=" CD2 LEU C 144 "
    ideal  model  delta    sigma   weight residual
    1.521  1.472  0.049 3.30e-02 9.18e+02 2.18e+00
  bond pdb=" CA  ILE A 146 "
       pdb=" CB  ILE A 146 "
    ideal  model  delta    sigma   weight residual
    1.549  1.525  0.024 1.88e-02 2.83e+03 1.56e+00
  bond pdb=" CA  ILE C 146 "
       pdb=" CB  ILE C 146 "
    ideal  model  delta    sigma   weight residual
    1.549  1.525  0.023 1.88e-02 2.83e+03 1.56e+00
  ... (remaining 3307 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 4022
        1.20 -     2.41: 412
        2.41 -     3.61: 45
        3.61 -     4.82: 19
        4.82 -     6.02: 5
  Bond angle restraints: 4503
  Sorted by residual:
  angle pdb=" C   LEU A 144 "
        pdb=" N   ASN A 145 "
        pdb=" CA  ASN A 145 "
      ideal   model   delta    sigma   weight residual
     122.82  127.69   -4.87 1.42e+00 4.96e-01 1.17e+01
  angle pdb=" C   LEU C 144 "
        pdb=" N   ASN C 145 "
        pdb=" CA  ASN C 145 "
      ideal   model   delta    sigma   weight residual
     122.82  127.65   -4.83 1.42e+00 4.96e-01 1.16e+01
  angle pdb=" C   LEU B 144 "
        pdb=" N   ASN B 145 "
        pdb=" CA  ASN B 145 "
      ideal   model   delta    sigma   weight residual
     122.82  127.64   -4.82 1.42e+00 4.96e-01 1.15e+01
  angle pdb=" C   ARG A 140 "
        pdb=" CA  ARG A 140 "
        pdb=" CB  ARG A 140 "
      ideal   model   delta    sigma   weight residual
     111.86  107.99    3.87 1.34e+00 5.57e-01 8.33e+00
  angle pdb=" C   ARG C 140 "
        pdb=" CA  ARG C 140 "
        pdb=" CB  ARG C 140 "
      ideal   model   delta    sigma   weight residual
     111.86  108.01    3.85 1.34e+00 5.57e-01 8.25e+00
  ... (remaining 4498 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.50: 1767
       16.50 -    33.01: 201
       33.01 -    49.51: 15
       49.51 -    66.02: 9
       66.02 -    82.52: 3
  Dihedral angle restraints: 1995
    sinusoidal: 777
      harmonic: 1218
  Sorted by residual:
  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  157.02   22.98     0      5.00e+00 4.00e-02 2.11e+01
  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  157.02   22.98     0      5.00e+00 4.00e-02 2.11e+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  157.08   22.92     0      5.00e+00 4.00e-02 2.10e+01
  ... (remaining 1992 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 376
       0.053 -    0.107: 123
       0.107 -    0.160: 38
       0.160 -    0.213: 3
       0.213 -    0.266: 3
  Chirality restraints: 543
  Sorted by residual:
  chirality pdb=" CB  ILE A 186 "
            pdb=" CA  ILE A 186 "
            pdb=" CG1 ILE A 186 "
            pdb=" CG2 ILE A 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CB  ILE C 186 "
            pdb=" CA  ILE C 186 "
            pdb=" CG1 ILE C 186 "
            pdb=" CG2 ILE C 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CB  ILE B 186 "
            pdb=" CA  ILE B 186 "
            pdb=" CG1 ILE B 186 "
            pdb=" CG2 ILE B 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.75e+00
  ... (remaining 540 not shown)

  Planarity restraints: 558
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 143 "    0.012 2.00e-02 2.50e+03   8.59e-03 1.48e+00
        pdb=" CG  TYR A 143 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 143 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 143 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 143 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 143 "    0.002 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
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 143 "    0.011 2.00e-02 2.50e+03   8.55e-03 1.46e+00
        pdb=" CG  TYR B 143 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 143 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 143 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 143 "    0.001 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 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 143 "    0.011 2.00e-02 2.50e+03   8.48e-03 1.44e+00
        pdb=" CG  TYR C 143 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 143 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 143 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 143 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 143 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 143 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C 143 "    0.002 2.00e-02 2.50e+03
  ... (remaining 555 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 794
        2.79 -     3.32: 2924
        3.32 -     3.85: 5147
        3.85 -     4.37: 5723
        4.37 -     4.90: 11598
  Nonbonded interactions: 26186
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 236 "
            pdb=" O   HIS A 239 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OH  TYR C 236 "
            pdb=" O   HIS C 239 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OH  TYR B 236 "
            pdb=" O   HIS B 239 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OE2 GLU B 161 "
            pdb=" ND1 HIS C 239 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" ND1 HIS B 239 "
            pdb=" OE2 GLU A 161 "
     model   vdw
     2.347 3.120
  ... (remaining 26181 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:             4.300
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.010
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
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   0.050   3315  Z= 0.393
  Angle     :  0.803   6.025   4509  Z= 0.472
  Chirality :  0.059   0.266    543
  Planarity :  0.003   0.009    558
  Dihedral  : 14.226  82.523   1206
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 16.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.29 %
    Favored  : 85.71 %
  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: -5.99 (0.28), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.56 (0.21), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 140 
 TYR   0.021   0.003   TYR B 250 
 PHE   0.015   0.003   PHE C 213 
 HIS   0.005   0.002   HIS B 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00889 ( 3312)
  covalent geometry    : angle       0.80262 ( 4503)
  SS BOND              : bond        0.00737 (    3)
  SS BOND              : angle       0.74794 (    6)
  hydrogen bonds       : bond        0.14410 (   36)
  hydrogen bonds       : angle       8.18488 (  108)

*********************** 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
  31 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.099 
Fit side-chains
REVERT: B  161 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8092 (mm-30)
REVERT: B  192 MET cc_start: 0.8360 (mtt) cc_final: 0.8094 (mtp)
REVERT: B  210 MET cc_start: 0.8090 (mtt) cc_final: 0.7831 (mtt)
REVERT: B  220 LYS cc_start: 0.8308 (mttt) cc_final: 0.7985 (mtpt)
REVERT: A  161 GLU cc_start: 0.8660 (mm-30) cc_final: 0.7865 (mm-30)
REVERT: A  192 MET cc_start: 0.8610 (mtt) cc_final: 0.8296 (mtp)
REVERT: A  207 MET cc_start: 0.6981 (ttm) cc_final: 0.6779 (ttm)
REVERT: A  210 MET cc_start: 0.8415 (mtt) cc_final: 0.8180 (mtt)
REVERT: C  161 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7157 (mm-30)
REVERT: C  220 LYS cc_start: 0.8335 (mttt) cc_final: 0.7973 (mtpt)
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0777
  time to fit residues: 2.9614
Evaluate side-chains
  30 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    7.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
B 223 ASN
C 155 ASN
C 223 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.145655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.129174 restraints weight = 3771.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 2.33
r_work: 0.3911 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3796 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3315  Z= 0.195
  Angle     :  0.614   4.259   4509  Z= 0.351
  Chirality :  0.053   0.171    543
  Planarity :  0.002   0.017    558
  Dihedral  :  6.588  21.415    447
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.28 %
    Favored  : 89.72 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 12.43 %
    Favored  : 85.71 %
  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: -5.77 (0.28), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.39 (0.21), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 247 
 TYR   0.019   0.002   TYR A 143 
 PHE   0.007   0.002   PHE B 213 
 HIS   0.003   0.002   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 3312)
  covalent geometry    : angle       0.61444 ( 4503)
  SS BOND              : bond        0.00287 (    3)
  SS BOND              : angle       0.53582 (    6)
  hydrogen bonds       : bond        0.02177 (   36)
  hydrogen bonds       : angle       5.39039 (  108)

*********************** 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
  42 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.127 
Fit side-chains
REVERT: B  161 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8004 (mm-30)
REVERT: B  192 MET cc_start: 0.8428 (mtt) cc_final: 0.8193 (mtp)
REVERT: B  210 MET cc_start: 0.8419 (mtt) cc_final: 0.8169 (mtt)
REVERT: B  220 LYS cc_start: 0.8319 (mttt) cc_final: 0.7944 (mtpt)
REVERT: A  161 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8027 (mm-30)
REVERT: A  180 ARG cc_start: 0.7290 (ptp-170) cc_final: 0.6939 (ptp90)
REVERT: A  192 MET cc_start: 0.8814 (mtt) cc_final: 0.8539 (mtp)
REVERT: A  207 MET cc_start: 0.7234 (ttm) cc_final: 0.7013 (ttm)
REVERT: A  210 MET cc_start: 0.8555 (mtt) cc_final: 0.8285 (mtm)
REVERT: C  161 GLU cc_start: 0.7547 (mm-30) cc_final: 0.6756 (mm-30)
REVERT: C  220 LYS cc_start: 0.8373 (mttt) cc_final: 0.7966 (mtpt)
  outliers start: 7
  outliers final: 4
  residues processed: 40
  average time/residue: 0.0779
  time to fit residues: 3.7991
Evaluate side-chains
  38 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain A residue  175 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:    7.9990
   chunk 29 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 37 optimal weight:    0.1980
   chunk 27 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 9 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9980
   overall best weight:    2.8386

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

Flipped N/Q/H residues before XYZ refinement:
A 223 ASN
** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.135865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.118703 restraints weight = 3992.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3996 rms_B_bonded: 2.46
r_work: 0.3887 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3770 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3315  Z= 0.219
  Angle     :  0.606   4.145   4509  Z= 0.345
  Chirality :  0.053   0.173    543
  Planarity :  0.003   0.021    558
  Dihedral  :  6.458  21.333    447
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.53 %
    Favored  : 87.47 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 16.93 %
    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 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: -5.58 (0.29), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.25 (0.22), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 247 
 TYR   0.020   0.002   TYR A 143 
 PHE   0.009   0.002   PHE A 237 
 HIS   0.003   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 3312)
  covalent geometry    : angle       0.60644 ( 4503)
  SS BOND              : bond        0.00350 (    3)
  SS BOND              : angle       0.50428 (    6)
  hydrogen bonds       : bond        0.02068 (   36)
  hydrogen bonds       : angle       4.72260 (  108)

*********************** 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
  43 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 32
  time to evaluate  : 0.081 
Fit side-chains
REVERT: B  146 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8545 (pt)
REVERT: B  192 MET cc_start: 0.8440 (mtt) cc_final: 0.8230 (mtp)
REVERT: B  210 MET cc_start: 0.8384 (mtt) cc_final: 0.8120 (mtt)
REVERT: B  220 LYS cc_start: 0.8240 (mttt) cc_final: 0.7903 (mtpt)
REVERT: A  161 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8109 (mm-30)
REVERT: A  192 MET cc_start: 0.8800 (mtt) cc_final: 0.8543 (mtp)
REVERT: A  210 MET cc_start: 0.8627 (mtt) cc_final: 0.8334 (mtt)
REVERT: C  146 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8533 (pt)
REVERT: C  220 LYS cc_start: 0.8352 (mttt) cc_final: 0.7929 (mtpt)
  outliers start: 11
  outliers final: 7
  residues processed: 41
  average time/residue: 0.0708
  time to fit residues: 3.5457
Evaluate side-chains
  41 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  160 VAL
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 C residue  146 ILE
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  244 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:    8.9990
   chunk 16 optimal weight:    3.9990
   chunk 27 optimal weight:    7.9990
   chunk 11 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.133414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.115862 restraints weight = 4082.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3946 rms_B_bonded: 2.52
r_work: 0.3833 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3715 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.031   3315  Z= 0.278
  Angle     :  0.646   4.336   4509  Z= 0.369
  Chirality :  0.053   0.183    543
  Planarity :  0.003   0.021    558
  Dihedral  :  6.631  21.866    447
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.28 %
    Favored  : 88.72 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 17.46 %
    Favored  : 77.51 %
  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: -5.48 (0.30), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.17 (0.23), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 140 
 TYR   0.023   0.003   TYR A 143 
 PHE   0.010   0.003   PHE A 237 
 HIS   0.004   0.002   HIS A 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00636 ( 3312)
  covalent geometry    : angle       0.64582 ( 4503)
  SS BOND              : bond        0.00381 (    3)
  SS BOND              : angle       0.59128 (    6)
  hydrogen bonds       : bond        0.02109 (   36)
  hydrogen bonds       : angle       4.68251 (  108)

*********************** 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
  52 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 33
  time to evaluate  : 0.106 
Fit side-chains
REVERT: B  146 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8509 (pt)
REVERT: B  161 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8051 (mm-30)
REVERT: B  192 MET cc_start: 0.8445 (mtt) cc_final: 0.8220 (mtp)
REVERT: B  210 MET cc_start: 0.8432 (mtt) cc_final: 0.8005 (mtt)
REVERT: B  220 LYS cc_start: 0.8320 (mttt) cc_final: 0.7998 (mtpt)
REVERT: A  146 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8725 (pt)
REVERT: A  161 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8199 (mm-30)
REVERT: A  192 MET cc_start: 0.8817 (mtt) cc_final: 0.8578 (mtp)
REVERT: A  210 MET cc_start: 0.8564 (mtt) cc_final: 0.8309 (mtt)
REVERT: C  141 THR cc_start: 0.8974 (t) cc_final: 0.8701 (p)
REVERT: C  146 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8597 (pt)
REVERT: C  220 LYS cc_start: 0.8393 (mttt) cc_final: 0.7982 (mtpt)
  outliers start: 19
  outliers final: 9
  residues processed: 47
  average time/residue: 0.0673
  time to fit residues: 3.8516
Evaluate side-chains
  45 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 33
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain A residue  146 ILE
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  186 ILE
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  160 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 9 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
B 229 GLN
A 229 GLN
** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.139332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.121624 restraints weight = 3775.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.4066 rms_B_bonded: 2.57
r_work: 0.3953 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3832 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3315  Z= 0.132
  Angle     :  0.543   3.905   4509  Z= 0.310
  Chirality :  0.052   0.163    543
  Planarity :  0.002   0.021    558
  Dihedral  :  6.017  19.256    447
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 16.93 %
    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: -5.34 (0.30), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.06 (0.23), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 140 
 TYR   0.014   0.001   TYR A 143 
 PHE   0.007   0.001   PHE A 237 
 HIS   0.005   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3312)
  covalent geometry    : angle       0.54313 ( 4503)
  SS BOND              : bond        0.00229 (    3)
  SS BOND              : angle       0.37147 (    6)
  hydrogen bonds       : bond        0.01507 (   36)
  hydrogen bonds       : angle       4.44972 (  108)

*********************** 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
  50 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 33
  time to evaluate  : 0.091 
Fit side-chains
REVERT: B  129 LYS cc_start: 0.8288 (ptpp) cc_final: 0.8072 (ptmm)
REVERT: B  146 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8513 (pt)
REVERT: B  180 ARG cc_start: 0.7243 (ptp-170) cc_final: 0.6871 (ptm160)
REVERT: B  192 MET cc_start: 0.8373 (mtt) cc_final: 0.8096 (mtp)
REVERT: B  210 MET cc_start: 0.8454 (mtt) cc_final: 0.8055 (mtt)
REVERT: A  192 MET cc_start: 0.8786 (mtt) cc_final: 0.8579 (mtp)
REVERT: C  146 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8502 (pt)
REVERT: C  220 LYS cc_start: 0.8326 (mttt) cc_final: 0.7906 (mtpt)
  outliers start: 17
  outliers final: 7
  residues processed: 46
  average time/residue: 0.0777
  time to fit residues: 4.1940
Evaluate side-chains
  40 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  186 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 8 optimal weight:   10.0000
   chunk 16 optimal weight:    0.7980
   chunk 9 optimal weight:    8.9990
   chunk 18 optimal weight:    7.9990
   chunk 28 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 31 optimal weight:   10.0000
   chunk 19 optimal weight:    0.4980
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.148050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.129692 restraints weight = 3589.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.4137 rms_B_bonded: 2.57
r_work: 0.4022 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3898 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.2453

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     :  0.563   4.709   4509  Z= 0.320
  Chirality :  0.052   0.167    543
  Planarity :  0.002   0.021    558
  Dihedral  :  5.866  18.855    447
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 15.61 %
    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: -5.23 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.98 (0.23), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 180 
 TYR   0.014   0.002   TYR A 143 
 PHE   0.007   0.002   PHE A 237 
 HIS   0.005   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 3312)
  covalent geometry    : angle       0.56339 ( 4503)
  SS BOND              : bond        0.00238 (    3)
  SS BOND              : angle       0.34863 (    6)
  hydrogen bonds       : bond        0.01536 (   36)
  hydrogen bonds       : angle       4.39529 (  108)

*********************** 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
  51 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 32
  time to evaluate  : 0.126 
Fit side-chains
REVERT: B  129 LYS cc_start: 0.8459 (ptpp) cc_final: 0.8254 (ptmm)
REVERT: B  146 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8468 (pt)
REVERT: B  180 ARG cc_start: 0.7337 (ptp-170) cc_final: 0.7080 (ptm160)
REVERT: B  210 MET cc_start: 0.8521 (mtt) cc_final: 0.8099 (mtt)
REVERT: A  146 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8634 (pt)
REVERT: A  192 MET cc_start: 0.8791 (mtt) cc_final: 0.8562 (mtp)
REVERT: C  146 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8490 (pt)
REVERT: C  220 LYS cc_start: 0.8381 (mttt) cc_final: 0.7963 (mtpt)
  outliers start: 19
  outliers final: 11
  residues processed: 48
  average time/residue: 0.0836
  time to fit residues: 4.7447
Evaluate side-chains
  45 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 31
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain A residue  146 ILE
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  186 ILE
Chi-restraints excluded: chain A residue  193 LYS
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  186 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   chunk 1 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.149231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.131104 restraints weight = 3649.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.4057 rms_B_bonded: 2.52
r_work: 0.3945 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3827 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.2611

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= 0.135
  Angle     :  0.565   4.810   4509  Z= 0.321
  Chirality :  0.051   0.168    543
  Planarity :  0.002   0.022    558
  Dihedral  :  5.767  18.404    447
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 15.87 %
    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 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: -5.12 (0.32), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.89 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 180 
 TYR   0.014   0.001   TYR A 143 
 PHE   0.008   0.002   PHE A 237 
 HIS   0.005   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 3312)
  covalent geometry    : angle       0.56511 ( 4503)
  SS BOND              : bond        0.00226 (    3)
  SS BOND              : angle       0.36068 (    6)
  hydrogen bonds       : bond        0.01481 (   36)
  hydrogen bonds       : angle       4.37890 (  108)

*********************** 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
  48 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 29
  time to evaluate  : 0.135 
Fit side-chains
REVERT: B  146 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8464 (pt)
REVERT: B  180 ARG cc_start: 0.7452 (ptp-170) cc_final: 0.7175 (ptm160)
REVERT: B  210 MET cc_start: 0.8481 (mtt) cc_final: 0.8081 (mtt)
REVERT: A  141 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8606 (p)
REVERT: A  146 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8626 (pt)
REVERT: C  146 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8455 (pt)
REVERT: C  220 LYS cc_start: 0.8406 (mttt) cc_final: 0.7985 (mtpt)
  outliers start: 19
  outliers final: 12
  residues processed: 45
  average time/residue: 0.0852
  time to fit residues: 4.6070
Evaluate side-chains
  45 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 29
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  146 ILE
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  186 ILE
Chi-restraints excluded: chain A residue  193 LYS
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  178 LYS
Chi-restraints excluded: chain C residue  186 ILE
Chi-restraints excluded: chain C residue  244 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   chunk 11 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 37 optimal weight:    0.3980
   chunk 29 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 22 optimal weight:    8.9990
   chunk 35 optimal weight:    6.9990
   chunk 34 optimal weight:    7.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    3.4788

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

Flipped N/Q/H residues before XYZ refinement:
** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.141464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.123730 restraints weight = 3844.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3968 rms_B_bonded: 2.56
r_work: 0.3850 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3732 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032   3315  Z= 0.258
  Angle     :  0.648   4.648   4509  Z= 0.370
  Chirality :  0.053   0.181    543
  Planarity :  0.003   0.020    558
  Dihedral  :  6.244  20.826    447
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.53 %
    Favored  : 87.47 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 15.34 %
    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: -5.20 (0.32), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.96 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 140 
 TYR   0.024   0.003   TYR A 143 
 PHE   0.011   0.003   PHE C 237 
 HIS   0.004   0.002   HIS B 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00590 ( 3312)
  covalent geometry    : angle       0.64857 ( 4503)
  SS BOND              : bond        0.00359 (    3)
  SS BOND              : angle       0.51617 (    6)
  hydrogen bonds       : bond        0.02000 (   36)
  hydrogen bonds       : angle       4.55382 (  108)

*********************** 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
  52 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 33
  time to evaluate  : 0.101 
Fit side-chains
REVERT: B  146 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8525 (pt)
REVERT: B  180 ARG cc_start: 0.7490 (ptp-170) cc_final: 0.7187 (ptm160)
REVERT: B  210 MET cc_start: 0.8486 (mtt) cc_final: 0.8055 (mtt)
REVERT: A  141 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8702 (p)
REVERT: A  146 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8699 (pt)
REVERT: C  220 LYS cc_start: 0.8427 (mttt) cc_final: 0.8043 (mtpt)
  outliers start: 19
  outliers final: 12
  residues processed: 49
  average time/residue: 0.0874
  time to fit residues: 5.1017
Evaluate side-chains
  47 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 32
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  146 ILE
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  186 ILE
Chi-restraints excluded: chain A residue  193 LYS
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  186 ILE
Chi-restraints excluded: chain C residue  244 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 30 optimal weight:    6.9990
   chunk 12 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 35 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9980
   chunk 25 optimal weight:    4.9990
   chunk 34 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    2.7986

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

Flipped N/Q/H residues before XYZ refinement:
** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.143377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.125410 restraints weight = 3787.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.3982 rms_B_bonded: 2.55
r_work: 0.3872 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3752 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   3315  Z= 0.211
  Angle     :  0.621   4.956   4509  Z= 0.354
  Chirality :  0.053   0.177    543
  Planarity :  0.002   0.021    558
  Dihedral  :  6.189  20.257    447
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 16.40 %
    Favored  : 78.31 %
  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: -5.24 (0.32), 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
 ARG   0.001   0.000   ARG A 140 
 TYR   0.021   0.002   TYR A 143 
 PHE   0.009   0.002   PHE C 237 
 HIS   0.004   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 3312)
  covalent geometry    : angle       0.62117 ( 4503)
  SS BOND              : bond        0.00314 (    3)
  SS BOND              : angle       0.53931 (    6)
  hydrogen bonds       : bond        0.01857 (   36)
  hydrogen bonds       : angle       4.60002 (  108)

*********************** 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
  49 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 29
  time to evaluate  : 0.133 
Fit side-chains
REVERT: B  146 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8460 (pt)
REVERT: B  180 ARG cc_start: 0.7571 (ptp-170) cc_final: 0.7265 (ptm160)
REVERT: B  210 MET cc_start: 0.8493 (mtt) cc_final: 0.8063 (mtt)
REVERT: A  146 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8674 (pt)
REVERT: C  146 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8534 (pt)
REVERT: C  220 LYS cc_start: 0.8440 (mttt) cc_final: 0.8045 (mtpt)
  outliers start: 20
  outliers final: 11
  residues processed: 47
  average time/residue: 0.0813
  time to fit residues: 4.5627
Evaluate side-chains
  43 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 29
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  146 ILE
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  186 ILE
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  186 ILE
Chi-restraints excluded: chain C residue  244 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0870
   chunk 12 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   chunk 15 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 7 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    1.3562

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.152016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.134629 restraints weight = 3740.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.4080 rms_B_bonded: 2.45
r_work: 0.3967 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3848 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.2848

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= 0.125
  Angle     :  0.567   5.071   4509  Z= 0.323
  Chirality :  0.052   0.158    543
  Planarity :  0.002   0.023    558
  Dihedral  :  5.816  19.837    447
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 17.20 %
    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 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: -5.19 (0.32), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.95 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 140 
 TYR   0.014   0.001   TYR A 143 
 PHE   0.007   0.001   PHE A 237 
 HIS   0.005   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3312)
  covalent geometry    : angle       0.56722 ( 4503)
  SS BOND              : bond        0.00200 (    3)
  SS BOND              : angle       0.38488 (    6)
  hydrogen bonds       : bond        0.01552 (   36)
  hydrogen bonds       : angle       4.52846 (  108)

********************** 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
  45 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 30
  time to evaluate  : 0.079 
Fit side-chains
REVERT: B  146 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8429 (pt)
REVERT: B  180 ARG cc_start: 0.7502 (ptp-170) cc_final: 0.7196 (ptm160)
REVERT: B  210 MET cc_start: 0.8469 (mtt) cc_final: 0.8040 (mtt)
REVERT: A  146 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8621 (pt)
REVERT: C  146 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8469 (pt)
REVERT: C  220 LYS cc_start: 0.8362 (mttt) cc_final: 0.7978 (mtpt)
  outliers start: 15
  outliers final: 11
  residues processed: 44
  average time/residue: 0.0909
  time to fit residues: 4.6452
Evaluate side-chains
  44 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 30
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  146 ILE
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  186 ILE
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  186 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 14 optimal weight:    0.4980
   chunk 22 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 34 optimal weight:    8.9990
   chunk 16 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 4 optimal weight:    8.9990
   overall best weight:    2.4386

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

Flipped N/Q/H residues before XYZ refinement:
** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.147140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.129781 restraints weight = 3678.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.4181 rms_B_bonded: 2.45
r_work: 0.4069 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3944 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.2798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3315  Z= 0.190
  Angle     :  0.621   5.733   4509  Z= 0.352
  Chirality :  0.053   0.176    543
  Planarity :  0.002   0.023    558
  Dihedral  :  6.032  20.835    447
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.28 %
    Favored  : 88.72 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 17.99 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -5.18 (0.32), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.94 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 180 
 TYR   0.023   0.002   TYR A 143 
 PHE   0.009   0.002   PHE A 237 
 HIS   0.004   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 3312)
  covalent geometry    : angle       0.62095 ( 4503)
  SS BOND              : bond        0.00267 (    3)
  SS BOND              : angle       0.45186 (    6)
  hydrogen bonds       : bond        0.01780 (   36)
  hydrogen bonds       : angle       4.53651 (  108)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 985.19 seconds
wall clock time: 17 minutes 39.90 seconds (1059.90 seconds total)