Starting phenix.real_space_refine
on Fri Dec 27 06:47:25 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qwm_14189/12_2024/7qwm_14189.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qwm_14189/12_2024/7qwm_14189.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qwm_14189/12_2024/7qwm_14189.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qwm_14189/12_2024/7qwm_14189.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qwm_14189/12_2024/7qwm_14189.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qwm_14189/12_2024/7qwm_14189.cif"
  }
  resolution = 2.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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    2079      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 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 3255
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 132}
    Chain: "C"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 132}
  Time building chain proxies: 3.10, per 1000 atoms: 0.95
  Number of scatterers: 3255
  At special positions: 0
  Unit cell: (87.874, 114.402, 36.476, 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    2079      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 253 " distance=2.04
    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: 0.72
  Conformation dependent library (CDL) restraints added in 352.0 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 13 sheets defined
      0.0% alpha, 66.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 126
      removed outlier: 6.170A  pdb=" N   ILE A 121 " --> pdb=" O   ASP B 122 " (cutoff:3.500A)
      removed outlier: 8.589A  pdb=" N   LYS B 124 " --> pdb=" O   ILE A 121 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   VAL A 123 " --> pdb=" O   LYS B 124 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   ILE B 126 " --> pdb=" O   VAL A 123 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   TYR A 125 " --> pdb=" O   ILE B 126 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   ILE B 121 " --> pdb=" O   ASP C 122 " (cutoff:3.500A)
      removed outlier: 8.746A  pdb=" N   LYS C 124 " --> pdb=" O   ILE B 121 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   VAL B 123 " --> pdb=" O   LYS C 124 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   ILE C 126 " --> pdb=" O   VAL B 123 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   TYR B 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 'A' and resid 129 through 130
      removed outlier: 6.812A  pdb=" N   LYS A 129 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   LYS B 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 'A' and resid 133 through 138
      removed outlier: 6.415A  pdb=" N   SER A 134 " --> pdb=" O   TYR B 135 " (cutoff:3.500A)
      removed outlier: 7.772A  pdb=" N   VAL B 137 " --> pdb=" O   SER A 134 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   ASP A 136 " --> pdb=" O   VAL B 137 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   SER B 134 " --> pdb=" O   TYR C 135 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   VAL C 137 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   ASP B 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 'A' and resid 142 through 153
      removed outlier: 7.041A  pdb=" N   TYR A 143 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   LEU B 144 " --> pdb=" O   TYR A 143 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ASN A 145 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   TYR B 143 " --> pdb=" O   ILE C 142 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   LEU C 144 " --> pdb=" O   TYR B 143 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   ASN B 145 " --> pdb=" O   LEU C 144 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 160
      removed outlier: 6.477A  pdb=" N   TYR A 157 " --> pdb=" O   TYR B 158 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   VAL B 160 " --> pdb=" O   TYR A 157 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   SER A 159 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   TYR B 157 " --> pdb=" O   TYR C 158 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   VAL C 160 " --> pdb=" O   TYR B 157 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   SER B 159 " --> pdb=" O   VAL C 160 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 163 through 176
      removed outlier: 6.973A  pdb=" N   SER A 172 " --> pdb=" O   PHE B 171 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   LYS B 173 " --> pdb=" O   SER A 172 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   SER B 172 " --> pdb=" O   PHE C 171 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   LYS C 173 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 180 through 182
      removed outlier: 6.438A  pdb=" N   ARG A 180 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   ARG B 180 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 187
      removed outlier: 6.229A  pdb=" N   ILE A 186 " --> pdb=" O   ILE B 187 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ILE B 186 " --> pdb=" O   ILE C 187 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 190 through 194
    Processing sheet with id=AB1, first strand: chain 'A' and resid 201 through 213
      removed outlier: 9.091A  pdb=" N   THR A 201 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
      removed outlier: 10.255A  pdb=" N   ALA B 204 " --> pdb=" O   THR A 201 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   ILE A 203 " --> pdb=" O   ALA B 204 " (cutoff:3.500A)
      removed outlier: 8.073A  pdb=" N   GLU B 206 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   GLU A 205 " --> pdb=" O   GLU B 206 " (cutoff:3.500A)
      removed outlier: 7.963A  pdb=" N   SER B 208 " --> pdb=" O   GLU A 205 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   MET A 207 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   MET B 210 " --> pdb=" O   MET A 207 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   TYR A 209 " --> pdb=" O   MET B 210 " (cutoff:3.500A)
      removed outlier: 7.702A  pdb=" N   ASP B 212 " --> pdb=" O   TYR A 209 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   TYR A 211 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
      removed outlier: 9.079A  pdb=" N   THR B 201 " --> pdb=" O   VAL C 202 " (cutoff:3.500A)
      removed outlier: 10.333A  pdb=" N   ALA C 204 " --> pdb=" O   THR B 201 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   ILE B 203 " --> pdb=" O   ALA C 204 " (cutoff:3.500A)
      removed outlier: 8.353A  pdb=" N   GLU C 206 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   GLU B 205 " --> pdb=" O   GLU C 206 " (cutoff:3.500A)
      removed outlier: 7.834A  pdb=" N   SER C 208 " --> pdb=" O   GLU B 205 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   MET B 207 " --> pdb=" O   SER C 208 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   MET C 210 " --> pdb=" O   MET B 207 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   TYR B 209 " --> pdb=" O   MET C 210 " (cutoff:3.500A)
      removed outlier: 7.679A  pdb=" N   ASP C 212 " --> pdb=" O   TYR B 209 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   TYR B 211 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 216 through 219
      removed outlier: 6.073A  pdb=" N   LEU A 216 " --> pdb=" O   ILE B 217 " (cutoff:3.500A)
      removed outlier: 7.826A  pdb=" N   ILE B 219 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   SER A 218 " --> pdb=" O   ILE B 219 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   LEU B 216 " --> pdb=" O   ILE C 217 " (cutoff:3.500A)
      removed outlier: 7.858A  pdb=" N   ILE C 219 " --> pdb=" O   LEU B 216 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   SER B 218 " --> pdb=" O   ILE C 219 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 222 through 245
      removed outlier: 9.072A  pdb=" N   HIS A 222 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
      removed outlier: 9.989A  pdb=" N   VAL B 225 " --> pdb=" O   HIS A 222 " (cutoff:3.500A)
      removed outlier: 8.899A  pdb=" N   ILE A 224 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 9.967A  pdb=" N   MET B 227 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
      removed outlier: 8.852A  pdb=" N   LEU A 226 " --> pdb=" O   MET B 227 " (cutoff:3.500A)
      removed outlier: 9.964A  pdb=" N   GLN B 229 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   MET A 228 " --> pdb=" O   GLN B 229 " (cutoff:3.500A)
      removed outlier: 8.982A  pdb=" N   THR B 231 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
      removed outlier: 8.919A  pdb=" N   VAL A 230 " --> pdb=" O   THR B 231 " (cutoff:3.500A)
      removed outlier: 5.820A  pdb=" N   THR B 233 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
      removed outlier: 8.518A  pdb=" N   VAL A 232 " --> pdb=" O   THR B 233 " (cutoff:3.500A)
      removed outlier: 9.710A  pdb=" N   THR B 235 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   THR A 234 " --> pdb=" O   THR B 235 " (cutoff:3.500A)
      removed outlier: 8.227A  pdb=" N   PHE B 237 " --> pdb=" O   THR A 234 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   TYR A 236 " --> pdb=" O   PHE B 237 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   HIS B 239 " --> pdb=" O   TYR A 236 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   GLY A 238 " --> pdb=" O   HIS B 239 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   GLU B 241 " --> pdb=" O   GLY A 238 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   SER A 240 " --> pdb=" O   GLU B 241 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   ILE B 243 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   GLN A 242 " --> pdb=" O   ILE B 243 " (cutoff:3.500A)
      removed outlier: 7.844A  pdb=" N   GLN B 245 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   SER A 244 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   VAL C 230 " --> pdb=" O   GLN B 229 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   THR B 231 " --> pdb=" O   VAL C 230 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   THR B 235 " --> pdb=" O   THR C 234 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   TYR C 236 " --> pdb=" O   THR B 235 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   PHE B 237 " --> pdb=" O   TYR C 236 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   GLY C 238 " --> pdb=" O   PHE B 237 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   HIS B 239 " --> pdb=" O   GLY C 238 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   SER C 240 " --> pdb=" O   HIS B 239 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   GLU B 241 " --> pdb=" O   SER C 240 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   GLN C 242 " --> pdb=" O   GLU B 241 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   ILE B 243 " --> pdb=" O   GLN C 242 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   SER C 244 " --> pdb=" O   ILE B 243 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   GLN B 245 " --> pdb=" O   SER C 244 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 248 through 253
      removed outlier: 6.806A  pdb=" N   GLN A 249 " --> pdb=" O   TYR B 250 " (cutoff:3.500A)
      removed outlier: 8.319A  pdb=" N   ASP B 252 " --> pdb=" O   GLN A 249 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   VAL A 251 " --> pdb=" O   ASP B 252 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   GLN B 249 " --> pdb=" O   TYR C 250 " (cutoff:3.500A)
      removed outlier: 8.285A  pdb=" N   ASP C 252 " --> pdb=" O   GLN B 249 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   VAL B 251 " --> pdb=" O   ASP C 252 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4

    56 hydrogen bonds defined for protein.
    168 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: 0.77

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 943
        1.33 -     1.46: 532
        1.46 -     1.58: 1798
        1.58 -     1.70: 0
        1.70 -     1.82: 36
  Bond restraints: 3309
  Sorted by residual:
  bond pdb=" N   ILE C 146 "
       pdb=" CA  ILE C 146 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.14e-02 7.69e+03 7.44e+00
  bond pdb=" CZ  ARG B 140 "
       pdb=" NH2 ARG B 140 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.59e+00
  bond pdb=" CZ  ARG B 247 "
       pdb=" NH2 ARG B 247 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.48e+00
  bond pdb=" CZ  ARG B 180 "
       pdb=" NH2 ARG B 180 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.47e+00
  bond pdb=" CZ  ARG C 140 "
       pdb=" NH2 ARG C 140 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.44e+00
  ... (remaining 3304 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 3130
        1.82 -     3.63: 1076
        3.63 -     5.45: 239
        5.45 -     7.26: 44
        7.26 -     9.08: 8
  Bond angle restraints: 4497
  Sorted by residual:
  angle pdb=" N   THR C 231 "
        pdb=" CA  THR C 231 "
        pdb=" C   THR C 231 "
      ideal   model   delta    sigma   weight residual
     112.45  121.41   -8.96 1.39e+00 5.18e-01 4.16e+01
  angle pdb=" CB  ASN B 183 "
        pdb=" CG  ASN B 183 "
        pdb=" ND2 ASN B 183 "
      ideal   model   delta    sigma   weight residual
     116.40  107.32    9.08 1.50e+00 4.44e-01 3.66e+01
  angle pdb=" N   GLN B 138 "
        pdb=" CA  GLN B 138 "
        pdb=" C   GLN B 138 "
      ideal   model   delta    sigma   weight residual
     108.60  117.03   -8.43 1.46e+00 4.69e-01 3.33e+01
  angle pdb=" CA  ASN C 145 "
        pdb=" CB  ASN C 145 "
        pdb=" CG  ASN C 145 "
      ideal   model   delta    sigma   weight residual
     112.60  118.24   -5.64 1.00e+00 1.00e+00 3.18e+01
  angle pdb=" CA  ASN B 183 "
        pdb=" CB  ASN B 183 "
        pdb=" CG  ASN B 183 "
      ideal   model   delta    sigma   weight residual
     112.60  118.15   -5.55 1.00e+00 1.00e+00 3.08e+01
  ... (remaining 4492 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.90: 1782
       14.90 -    29.81: 164
       29.81 -    44.71: 28
       44.71 -    59.61: 13
       59.61 -    74.51: 8
  Dihedral angle restraints: 1995
    sinusoidal: 777
      harmonic: 1218
  Sorted by residual:
  dihedral pdb=" CA  GLU A 206 "
           pdb=" C   GLU A 206 "
           pdb=" N   MET A 207 "
           pdb=" CA  MET A 207 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.23   29.77     0      5.00e+00 4.00e-02 3.54e+01
  dihedral pdb=" CA  GLU C 206 "
           pdb=" C   GLU C 206 "
           pdb=" N   MET C 207 "
           pdb=" CA  MET C 207 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.26   29.74     0      5.00e+00 4.00e-02 3.54e+01
  dihedral pdb=" CA  GLU B 206 "
           pdb=" C   GLU B 206 "
           pdb=" N   MET B 207 "
           pdb=" CA  MET B 207 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.11   28.89     0      5.00e+00 4.00e-02 3.34e+01
  ... (remaining 1992 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 415
       0.112 -    0.224: 104
       0.224 -    0.337: 13
       0.337 -    0.449: 5
       0.449 -    0.561: 3
  Chirality restraints: 540
  Sorted by residual:
  chirality pdb=" CA  THR A 231 "
            pdb=" N   THR A 231 "
            pdb=" C   THR A 231 "
            pdb=" CB  THR A 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.96    0.56 2.00e-01 2.50e+01 7.87e+00
  chirality pdb=" CA  THR C 231 "
            pdb=" N   THR C 231 "
            pdb=" C   THR C 231 "
            pdb=" CB  THR C 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.01    0.51 2.00e-01 2.50e+01 6.59e+00
  chirality pdb=" CA  LYS B 193 "
            pdb=" N   LYS B 193 "
            pdb=" C   LYS B 193 "
            pdb=" CB  LYS B 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.14e+00
  ... (remaining 537 not shown)

  Planarity restraints: 558
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 250 "    0.056 2.00e-02 2.50e+03   3.68e-02 2.71e+01
        pdb=" CG  TYR A 250 "    0.001 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 250 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 250 "   -0.028 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 250 "   -0.029 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 250 "   -0.030 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 250 "   -0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR A 250 "    0.066 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 171 "    0.053 2.00e-02 2.50e+03   3.25e-02 1.85e+01
        pdb=" CG  PHE A 171 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 171 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 171 "   -0.020 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 171 "    0.012 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 171 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 171 "    0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 248 "   -0.054 2.00e-02 2.50e+03   2.93e-02 1.71e+01
        pdb=" CG  TYR B 248 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 248 "    0.030 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 248 "    0.017 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 248 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 248 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 248 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR B 248 "   -0.044 2.00e-02 2.50e+03
  ... (remaining 555 not shown)

  Histogram of nonbonded interaction distances:
        2.50 -     2.98: 1535
        2.98 -     3.46: 2771
        3.46 -     3.94: 5653
        3.94 -     4.42: 5664
        4.42 -     4.90: 10689
  Nonbonded interactions: 26312
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 120 "
            pdb=" OE2 GLU B 161 "
     model   vdw
     2.502 3.040
  nonbonded pdb=" OG  SER B 120 "
            pdb=" OE2 GLU C 161 "
     model   vdw
     2.570 3.040
  nonbonded pdb=" O   GLY A 127 "
            pdb=" OH  TYR B 248 "
     model   vdw
     2.631 3.040
  nonbonded pdb=" O   GLY B 127 "
            pdb=" OH  TYR C 248 "
     model   vdw
     2.658 3.040
  nonbonded pdb=" OE1 GLN B 229 "
            pdb=" OG  SER B 240 "
     model   vdw
     2.665 3.040
  ... (remaining 26307 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  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:             1.520
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.730
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
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      :  0.012   0.038   3309  Z= 0.799
  Angle     :  1.929   9.079   4497  Z= 1.266
  Chirality :  0.107   0.561    540
  Planarity :  0.011   0.043    558
  Dihedral  : 13.263  74.511   1206
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 0.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Cbeta Deviations :  0.77 %
  Peptide Plane:
    Cis-proline     : 50.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.89 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.19 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS C 239 
 PHE   0.053   0.012   PHE A 171 
 TYR   0.066   0.015   TYR A 250 
 ARG   0.007   0.002   ARG C 247 

*********************** 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
  119 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 LYS cc_start: 0.7553 (mttt) cc_final: 0.7236 (mttm)
REVERT: A  145 ASN cc_start: 0.7161 (m-40) cc_final: 0.6885 (m-40)
REVERT: B  140 ARG cc_start: 0.6423 (mtt-85) cc_final: 0.6198 (mmm-85)
REVERT: B  173 LYS cc_start: 0.7358 (tttt) cc_final: 0.7007 (tttt)
REVERT: B  196 ASP cc_start: 0.7314 (t0) cc_final: 0.6969 (t0)
REVERT: B  202 VAL cc_start: 0.8110 (t) cc_final: 0.7900 (t)
REVERT: B  205 GLU cc_start: 0.6530 (mt-10) cc_final: 0.5932 (mt-10)
REVERT: C  140 ARG cc_start: 0.6769 (mtt-85) cc_final: 0.6345 (mmm-85)
REVERT: C  159 SER cc_start: 0.8232 (t) cc_final: 0.8013 (m)
REVERT: C  173 LYS cc_start: 0.7555 (tttt) cc_final: 0.7220 (tttt)
REVERT: C  196 ASP cc_start: 0.7459 (t0) cc_final: 0.7004 (t0)
REVERT: C  205 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6126 (mt-10)
REVERT: C  210 MET cc_start: 0.7267 (mtt) cc_final: 0.7044 (mtp)
REVERT: C  246 GLU cc_start: 0.7185 (mt-10) cc_final: 0.5886 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 1.1064
  time to fit residues: 135.2371
Evaluate side-chains
  86 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 10 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 30 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 18 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
B 164 ASN
B 194 GLN
C 194 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   3309  Z= 0.221
  Angle     :  0.682   8.237   4497  Z= 0.372
  Chirality :  0.055   0.130    540
  Planarity :  0.003   0.014    558
  Dihedral  :  7.140  22.281    447
  Min Nonbonded Distance : 2.658

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 11.11 %
    Favored  : 86.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 50.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.74 (0.34), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.08 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.002   HIS C 239 
 PHE   0.014   0.003   PHE B 213 
 TYR   0.016   0.002   TYR A 248 
 ARG   0.003   0.000   ARG A 247 

*********************** 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
  103 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 LEU cc_start: 0.8285 (mp) cc_final: 0.7992 (mt)
REVERT: A  171 PHE cc_start: 0.7693 (m-80) cc_final: 0.7474 (m-80)
REVERT: A  178 LYS cc_start: 0.6569 (tttt) cc_final: 0.6225 (mttp)
REVERT: A  180 ARG cc_start: 0.6215 (ttm-80) cc_final: 0.5708 (mmt-90)
REVERT: A  205 GLU cc_start: 0.6740 (mt-10) cc_final: 0.5900 (tt0)
REVERT: B  140 ARG cc_start: 0.6479 (mtt-85) cc_final: 0.6184 (mmm-85)
REVERT: B  161 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7246 (mt-10)
REVERT: B  205 GLU cc_start: 0.6601 (mt-10) cc_final: 0.5957 (mm-30)
REVERT: B  207 MET cc_start: 0.6162 (OUTLIER) cc_final: 0.5466 (mmm)
REVERT: C  140 ARG cc_start: 0.6751 (mtt-85) cc_final: 0.6354 (mmm-85)
REVERT: C  145 ASN cc_start: 0.6858 (m-40) cc_final: 0.6598 (m110)
REVERT: C  161 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7111 (mt-10)
REVERT: C  162 VAL cc_start: 0.8184 (t) cc_final: 0.7732 (m)
REVERT: C  191 ASP cc_start: 0.7732 (t0) cc_final: 0.7530 (t70)
REVERT: C  205 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6166 (mt-10)
REVERT: C  246 GLU cc_start: 0.7218 (mt-10) cc_final: 0.5943 (mp0)
  outliers start: 8
  outliers final: 1
  residues processed: 97
  average time/residue: 1.2806
  time to fit residues: 127.3252
Evaluate side-chains
  90 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain B residue  207 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 9 optimal weight:   30.0000
   chunk 35 optimal weight:    8.9990
   chunk 38 optimal weight:   10.0000
   chunk 31 optimal weight:    9.9990
   chunk 12 optimal weight:    9.9990
   chunk 28 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   overall best weight:    6.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.088   3309  Z= 0.516
  Angle     :  0.848   8.055   4497  Z= 0.471
  Chirality :  0.060   0.196    540
  Planarity :  0.004   0.027    558
  Dihedral  :  7.499  26.430    447
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 13.49 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 50.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.88 (0.34), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.18 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS A 222 
 PHE   0.019   0.004   PHE A 237 
 TYR   0.021   0.003   TYR B 143 
 ARG   0.005   0.001   ARG C 247 

*********************** 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
  102 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: A  162 VAL cc_start: 0.7926 (t) cc_final: 0.7391 (m)
REVERT: A  180 ARG cc_start: 0.6336 (ttm-80) cc_final: 0.5699 (mmt-90)
REVERT: A  193 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7477 (mtpp)
REVERT: A  205 GLU cc_start: 0.6891 (mt-10) cc_final: 0.5961 (tt0)
REVERT: B  140 ARG cc_start: 0.6459 (mtt-85) cc_final: 0.6161 (mmm-85)
REVERT: B  161 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7355 (mt-10)
REVERT: B  205 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6000 (mm-30)
REVERT: B  207 MET cc_start: 0.6260 (OUTLIER) cc_final: 0.5586 (mmm)
REVERT: C  140 ARG cc_start: 0.6999 (mtt-85) cc_final: 0.6572 (mmm-85)
REVERT: C  161 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7179 (mt-10)
REVERT: C  205 GLU cc_start: 0.6826 (mt-10) cc_final: 0.6371 (mt-10)
  outliers start: 13
  outliers final: 5
  residues processed: 94
  average time/residue: 1.3880
  time to fit residues: 133.5413
Evaluate side-chains
  94 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  193 LYS
Chi-restraints excluded: chain B residue  193 LYS
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain C residue  139 LYS
Chi-restraints excluded: chain C residue  193 LYS
Chi-restraints excluded: chain C residue  227 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 18 optimal weight:    7.9990
   chunk 3 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   chunk 37 optimal weight:    0.0030
   chunk 33 optimal weight:    0.5980
   chunk 10 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 21 optimal weight:    9.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.4794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3309  Z= 0.181
  Angle     :  0.601   6.491   4497  Z= 0.329
  Chirality :  0.053   0.133    540
  Planarity :  0.002   0.019    558
  Dihedral  :  6.789  23.050    447
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 15.87 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 50.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.86 (0.34), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.17 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS C 239 
 PHE   0.011   0.002   PHE A 237 
 TYR   0.012   0.001   TYR A 248 
 ARG   0.006   0.001   ARG B 180 

*********************** 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
  103 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 LYS cc_start: 0.7897 (mttt) cc_final: 0.7596 (mppt)
REVERT: A  150 LEU cc_start: 0.8320 (mp) cc_final: 0.7975 (mt)
REVERT: A  162 VAL cc_start: 0.7934 (t) cc_final: 0.7459 (m)
REVERT: A  180 ARG cc_start: 0.6351 (ttm-80) cc_final: 0.5768 (mmt-90)
REVERT: A  193 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7348 (mtpp)
REVERT: A  205 GLU cc_start: 0.6862 (mt-10) cc_final: 0.6081 (tt0)
REVERT: B  140 ARG cc_start: 0.6448 (mtt-85) cc_final: 0.6180 (mmm-85)
REVERT: B  162 VAL cc_start: 0.7904 (t) cc_final: 0.7333 (m)
REVERT: B  205 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6129 (mm-30)
REVERT: B  207 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.5581 (mmm)
REVERT: C  139 LYS cc_start: 0.7469 (mttm) cc_final: 0.6988 (mppt)
REVERT: C  140 ARG cc_start: 0.6823 (mtt-85) cc_final: 0.6456 (mmm-85)
REVERT: C  161 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7222 (mt-10)
REVERT: C  162 VAL cc_start: 0.8159 (t) cc_final: 0.7550 (m)
REVERT: C  205 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6446 (mt-10)
REVERT: C  246 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6046 (mp0)
  outliers start: 11
  outliers final: 2
  residues processed: 100
  average time/residue: 1.3728
  time to fit residues: 140.7129
Evaluate side-chains
  95 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  193 LYS
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain C residue  193 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 32 optimal weight:    8.9990
   chunk 26 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 9 optimal weight:   20.0000
   chunk 12 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 22 optimal weight:    9.9990
   overall best weight:    1.7786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3309  Z= 0.189
  Angle     :  0.583   5.550   4497  Z= 0.325
  Chirality :  0.053   0.128    540
  Planarity :  0.002   0.017    558
  Dihedral  :  6.569  23.090    447
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 16.40 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 50.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.86 (0.34), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.17 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS C 239 
 PHE   0.012   0.002   PHE A 237 
 TYR   0.012   0.002   TYR C 197 
 ARG   0.006   0.001   ARG B 180 

*********************** 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
  96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: A  162 VAL cc_start: 0.7915 (t) cc_final: 0.7450 (m)
REVERT: A  180 ARG cc_start: 0.6404 (ttm-80) cc_final: 0.5785 (mmt-90)
REVERT: A  193 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7537 (mtpp)
REVERT: A  205 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6150 (tt0)
REVERT: B  140 ARG cc_start: 0.6443 (mtt-85) cc_final: 0.6166 (mmm-85)
REVERT: B  162 VAL cc_start: 0.7882 (t) cc_final: 0.7337 (m)
REVERT: B  193 LYS cc_start: 0.7910 (mtmt) cc_final: 0.7693 (mtmt)
REVERT: B  205 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6137 (mm-30)
REVERT: B  207 MET cc_start: 0.6221 (OUTLIER) cc_final: 0.5506 (mmm)
REVERT: C  140 ARG cc_start: 0.6788 (mtt-85) cc_final: 0.6409 (mmm-85)
REVERT: C  145 ASN cc_start: 0.6948 (OUTLIER) cc_final: 0.6399 (m110)
REVERT: C  161 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7245 (mt-10)
REVERT: C  205 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6540 (mt-10)
REVERT: C  246 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6026 (mp0)
  outliers start: 12
  outliers final: 3
  residues processed: 89
  average time/residue: 1.4116
  time to fit residues: 128.6409
Evaluate side-chains
  90 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  193 LYS
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain C residue  145 ASN
Chi-restraints excluded: chain C residue  193 LYS
Chi-restraints excluded: chain C residue  227 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 9 optimal weight:   30.0000
   chunk 37 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   chunk 17 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 12 optimal weight:    9.9990
   chunk 19 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 27 optimal weight:    4.9990
   overall best weight:    6.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.086   3309  Z= 0.458
  Angle     :  0.773   6.303   4497  Z= 0.431
  Chirality :  0.058   0.178    540
  Planarity :  0.004   0.021    558
  Dihedral  :  7.138  25.310    447
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.99 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 50.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.94 (0.34), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.23 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS A 222 
 PHE   0.018   0.004   PHE A 237 
 TYR   0.019   0.003   TYR B 143 
 ARG   0.005   0.001   ARG B 180 

*********************** 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
  99 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
REVERT: A  162 VAL cc_start: 0.7935 (t) cc_final: 0.7443 (m)
REVERT: A  180 ARG cc_start: 0.6431 (ttm-80) cc_final: 0.5745 (mmt-90)
REVERT: A  193 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7528 (mtpp)
REVERT: A  205 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6101 (tt0)
REVERT: B  140 ARG cc_start: 0.6484 (mtt-85) cc_final: 0.6188 (mmm-85)
REVERT: B  162 VAL cc_start: 0.7823 (t) cc_final: 0.7303 (m)
REVERT: B  193 LYS cc_start: 0.7889 (mtmt) cc_final: 0.7681 (mtmt)
REVERT: B  207 MET cc_start: 0.6316 (OUTLIER) cc_final: 0.5589 (mmm)
REVERT: C  140 ARG cc_start: 0.6988 (mtt-85) cc_final: 0.6560 (mmm-85)
REVERT: C  145 ASN cc_start: 0.6993 (OUTLIER) cc_final: 0.6429 (m110)
REVERT: C  161 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7154 (mt-10)
REVERT: C  162 VAL cc_start: 0.8139 (t) cc_final: 0.7519 (m)
  outliers start: 12
  outliers final: 5
  residues processed: 91
  average time/residue: 1.4241
  time to fit residues: 132.6205
Evaluate side-chains
  95 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  193 LYS
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain C residue  139 LYS
Chi-restraints excluded: chain C residue  145 ASN
Chi-restraints excluded: chain C residue  193 LYS
Chi-restraints excluded: chain C residue  227 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 31 optimal weight:    7.9990
   chunk 37 optimal weight:    0.0970
   chunk 23 optimal weight:    7.9990
   chunk 22 optimal weight:    7.9990
   chunk 17 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0770
   chunk 11 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.9738

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.2875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   3309  Z= 0.147
  Angle     :  0.544   4.699   4497  Z= 0.304
  Chirality :  0.052   0.139    540
  Planarity :  0.002   0.024    558
  Dihedral  :  6.458  23.189    447
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 20.11 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 50.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.89 (0.34), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.19 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS C 239 
 PHE   0.009   0.002   PHE A 237 
 TYR   0.010   0.001   TYR A 248 
 ARG   0.007   0.001   ARG A 247 

*********************** 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
  97 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: A  162 VAL cc_start: 0.7915 (t) cc_final: 0.7428 (m)
REVERT: A  180 ARG cc_start: 0.6441 (ttm-80) cc_final: 0.5847 (mmt-90)
REVERT: A  193 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7602 (mtpp)
REVERT: A  196 ASP cc_start: 0.7048 (p0) cc_final: 0.6824 (p0)
REVERT: A  205 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6178 (tt0)
REVERT: B  140 ARG cc_start: 0.6512 (mtt-85) cc_final: 0.6213 (mmm-85)
REVERT: B  162 VAL cc_start: 0.7905 (t) cc_final: 0.7346 (m)
REVERT: B  205 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6140 (mm-30)
REVERT: B  207 MET cc_start: 0.6221 (mmt) cc_final: 0.5587 (mmm)
REVERT: C  140 ARG cc_start: 0.6714 (mtt-85) cc_final: 0.6428 (mmm-85)
REVERT: C  145 ASN cc_start: 0.6936 (OUTLIER) cc_final: 0.6379 (m110)
REVERT: C  161 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7213 (mt-10)
REVERT: C  205 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6568 (mt-10)
REVERT: C  207 MET cc_start: 0.6435 (mmm) cc_final: 0.6214 (mmm)
REVERT: C  208 SER cc_start: 0.7441 (m) cc_final: 0.7011 (t)
REVERT: C  231 THR cc_start: 0.5641 (OUTLIER) cc_final: 0.5397 (p)
REVERT: C  246 GLU cc_start: 0.7053 (mt-10) cc_final: 0.5716 (mp0)
  outliers start: 7
  outliers final: 0
  residues processed: 93
  average time/residue: 1.3693
  time to fit residues: 130.3182
Evaluate side-chains
  90 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 LYS
Chi-restraints excluded: chain C residue  145 ASN
Chi-restraints excluded: chain C residue  231 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   chunk 34 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 32 optimal weight:    8.9990
   chunk 35 optimal weight:    7.9990
   chunk 21 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 31 optimal weight:    7.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 194 GLN
B 194 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.2961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3309  Z= 0.134
  Angle     :  0.541   4.824   4497  Z= 0.302
  Chirality :  0.052   0.125    540
  Planarity :  0.002   0.035    558
  Dihedral  :  6.262  23.442    447
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 20.63 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 50.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.79 (0.35), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS C 239 
 PHE   0.009   0.002   PHE A 237 
 TYR   0.010   0.001   TYR B 248 
 ARG   0.009   0.001   ARG B 180 

*********************** 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
  92 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
REVERT: A  162 VAL cc_start: 0.7871 (t) cc_final: 0.7400 (m)
REVERT: A  180 ARG cc_start: 0.6452 (ttm-80) cc_final: 0.5903 (mmt-90)
REVERT: A  193 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7571 (mtpp)
REVERT: A  205 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6184 (tt0)
REVERT: B  140 ARG cc_start: 0.6465 (mtt-85) cc_final: 0.6189 (mmm-85)
REVERT: B  162 VAL cc_start: 0.7819 (t) cc_final: 0.7306 (m)
REVERT: B  205 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6146 (mm-30)
REVERT: B  207 MET cc_start: 0.6236 (OUTLIER) cc_final: 0.5642 (mmm)
REVERT: B  210 MET cc_start: 0.7375 (mtp) cc_final: 0.6886 (mtp)
REVERT: C  140 ARG cc_start: 0.6649 (mtt-85) cc_final: 0.6361 (mmm-85)
REVERT: C  161 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7161 (mt-10)
REVERT: C  205 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6571 (mt-10)
REVERT: C  246 GLU cc_start: 0.6876 (mt-10) cc_final: 0.5621 (mp0)
  outliers start: 5
  outliers final: 0
  residues processed: 88
  average time/residue: 1.4878
  time to fit residues: 133.8968
Evaluate side-chains
  88 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 86
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 LYS
Chi-restraints excluded: chain B residue  207 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0040
   chunk 23 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   chunk 38 optimal weight:    2.9990
   chunk 35 optimal weight:    9.9990
   chunk 30 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    2.5998

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

Flipped N/Q/H residues before XYZ refinement:
B 194 GLN
C 168 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.2837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3309  Z= 0.238
  Angle     :  0.636   5.522   4497  Z= 0.357
  Chirality :  0.053   0.135    540
  Planarity :  0.003   0.028    558
  Dihedral  :  6.540  24.780    447
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 20.11 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 50.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.81 (0.35), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.13 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS C 239 
 PHE   0.014   0.002   PHE A 237 
 TYR   0.015   0.002   TYR A 248 
 ARG   0.007   0.001   ARG B 180 

*********************** 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
  96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
REVERT: A  162 VAL cc_start: 0.7903 (t) cc_final: 0.7402 (m)
REVERT: A  180 ARG cc_start: 0.6430 (ttm-80) cc_final: 0.5794 (mmt-90)
REVERT: A  193 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7608 (mtpp)
REVERT: A  205 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6147 (tt0)
REVERT: B  140 ARG cc_start: 0.6461 (mtt-85) cc_final: 0.6164 (mmm-85)
REVERT: B  162 VAL cc_start: 0.7854 (t) cc_final: 0.7353 (m)
REVERT: B  207 MET cc_start: 0.6200 (OUTLIER) cc_final: 0.5557 (mmm)
REVERT: B  210 MET cc_start: 0.7431 (mtp) cc_final: 0.6827 (mtp)
REVERT: C  140 ARG cc_start: 0.6822 (mtt-85) cc_final: 0.6490 (mmm-85)
REVERT: C  145 ASN cc_start: 0.6849 (OUTLIER) cc_final: 0.6357 (m110)
REVERT: C  161 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7270 (mt-10)
REVERT: C  162 VAL cc_start: 0.8113 (t) cc_final: 0.7498 (m)
REVERT: C  168 GLN cc_start: 0.7608 (mt0) cc_final: 0.7242 (mt0)
REVERT: C  205 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6543 (mt-10)
REVERT: C  231 THR cc_start: 0.6016 (OUTLIER) cc_final: 0.5766 (p)
REVERT: C  246 GLU cc_start: 0.7090 (mt-10) cc_final: 0.5774 (mp0)
  outliers start: 5
  outliers final: 0
  residues processed: 92
  average time/residue: 1.4206
  time to fit residues: 133.6587
Evaluate side-chains
  93 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 89
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 LYS
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain C residue  145 ASN
Chi-restraints excluded: chain C residue  231 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    9.9990
   chunk 18 optimal weight:    8.9990
   chunk 24 optimal weight:    9.9990
   chunk 32 optimal weight:    0.4980
   chunk 9 optimal weight:   20.0000
   chunk 28 optimal weight:    0.4980
   chunk 4 optimal weight:    8.9990
   chunk 8 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    2.1986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3309  Z= 0.212
  Angle     :  0.618   6.490   4497  Z= 0.347
  Chirality :  0.053   0.131    540
  Planarity :  0.003   0.028    558
  Dihedral  :  6.599  25.011    447
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 20.90 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 50.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.84 (0.35), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.16 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS C 239 
 PHE   0.013   0.002   PHE A 237 
 TYR   0.013   0.002   TYR A 248 
 ARG   0.007   0.001   ARG B 180 

********************** 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
  91 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 87
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
REVERT: A  162 VAL cc_start: 0.7927 (t) cc_final: 0.7427 (m)
REVERT: A  180 ARG cc_start: 0.6433 (ttm-80) cc_final: 0.5826 (mmt-90)
REVERT: A  193 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7532 (mtpp)
REVERT: A  205 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6144 (tt0)
REVERT: B  140 ARG cc_start: 0.6445 (mtt-85) cc_final: 0.6138 (mmm-85)
REVERT: B  162 VAL cc_start: 0.7838 (t) cc_final: 0.7322 (m)
REVERT: B  207 MET cc_start: 0.6195 (OUTLIER) cc_final: 0.5571 (mmm)
REVERT: B  210 MET cc_start: 0.7426 (mtp) cc_final: 0.6844 (mtp)
REVERT: C  140 ARG cc_start: 0.6816 (mtt-85) cc_final: 0.6489 (mmm-85)
REVERT: C  145 ASN cc_start: 0.6830 (OUTLIER) cc_final: 0.6337 (m110)
REVERT: C  161 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7284 (mt-10)
REVERT: C  168 GLN cc_start: 0.7580 (mt0) cc_final: 0.7203 (mt0)
REVERT: C  205 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6544 (mt-10)
REVERT: C  246 GLU cc_start: 0.7094 (mt-10) cc_final: 0.5760 (mp0)
  outliers start: 4
  outliers final: 0
  residues processed: 88
  average time/residue: 1.4476
  time to fit residues: 130.1723
Evaluate side-chains
  87 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 84
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 LYS
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain C residue  145 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 27 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 15 optimal weight:    8.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 242 GLN
B 194 GLN
B 242 GLN
C 242 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.152366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.132714 restraints weight = 3151.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3772 rms_B_bonded: 1.40
r_work: 0.3667 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3575 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   3309  Z= 0.322
  Angle     :  0.674   5.388   4497  Z= 0.377
  Chirality :  0.054   0.144    540
  Planarity :  0.003   0.029    558
  Dihedral  :  6.838  25.276    447
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 21.43 %
    Favored  : 77.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 50.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.89 (0.35), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS C 239 
 PHE   0.017   0.003   PHE A 237 
 TYR   0.014   0.002   TYR B 143 
 ARG   0.006   0.001   ARG B 180 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2377.49 seconds
wall clock time: 43 minutes 12.87 seconds (2592.87 seconds total)