Starting phenix.real_space_refine
on Tue Mar  3 15:45:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f8v_31493/03_2026/7f8v_31493.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f8v_31493/03_2026/7f8v_31493.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f8v_31493/03_2026/7f8v_31493.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f8v_31493/03_2026/7f8v_31493.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f8v_31493/03_2026/7f8v_31493.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f8v_31493/03_2026/7f8v_31493.cif"
  }
  resolution = 3.3
  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=   0.003
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      53      5.16       5
     C    4224      2.51       5
     N    1127      2.21       5
     O    1197      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6601
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1748
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1748
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2347
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2347
          Classifications: {'peptide': 306}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 300}
    Chain: "C"
      Number of atoms: 245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 245
          Classifications: {'peptide': 33}
          Link IDs: {'PTRANS': 4, 'TRANS': 28}
    Chain: "E"
      Number of atoms: 133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 133
          Classifications: {'peptide': 17}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 15}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'PCA:plan-2': 1, 'GLU:plan': 4}
          Unresolved non-hydrogen planarities: 17
    Chain: "R"
      Number of atoms: 2128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2128
          Classifications: {'peptide': 275}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 13, 'TRANS': 261}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 15
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   ALA A 236 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA A 236 " occ=0.00
  Time building chain proxies: 1.64, per 1000 atoms: 0.25
  Number of scatterers: 6601
  At special positions: 0
  Unit cell: (110.77, 117.04, 81.51, 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      53     16.00
     O    1197      8.00
     N    1127      7.00
     C    4224      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 127 " - pdb=" SG  CYS R 205 " distance=2.04

  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: 0.70
  Conformation dependent library (CDL) restraints added in 260.1 milliseconds
  

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1592

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 11 sheets defined
      43.5% alpha, 16.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 29
    Processing helix  chain 'A' and resid 45 through 52
      removed outlier: 3.607A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 217
      removed outlier: 3.517A  pdb=" N   LYS A 211 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TRP A 212 " --> pdb=" O   ARG A 209 " (cutoff:3.500A)
      removed outlier: 5.078A  pdb=" N   ILE A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 5.370A  pdb=" N   HIS A 214 " --> pdb=" O   LYS A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 232
      removed outlier: 4.254A  pdb=" N   ASP A 232 " --> pdb=" O   SER A 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 229 through 232'
    Processing helix  chain 'A' and resid 242 through 256
    Processing helix  chain 'A' and resid 257 through 261
      removed outlier: 3.583A  pdb=" N   PHE A 260 " --> pdb=" O   ASN A 257 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   THR A 261 " --> pdb=" O   LYS A 258 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 257 through 261'
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 5.208A  pdb=" N   GLU A 277 " --> pdb=" O   ASP A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 310
    Processing helix  chain 'A' and resid 331 through 352
    Processing helix  chain 'C' and resid 30 through 45
    Processing helix  chain 'R' and resid 56 through 81
      removed outlier: 4.475A  pdb=" N   ASN R  72 " --> pdb=" O   SER R  68 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU R  81 " --> pdb=" O   VAL R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 87 through 107
    Processing helix  chain 'R' and resid 107 through 117
      removed outlier: 3.612A  pdb=" N   LEU R 113 " --> pdb=" O   PRO R 109 " (cutoff:3.500A)
      Proline residue:  R 114  - end of helix
    Processing helix  chain 'R' and resid 123 through 157
    Processing helix  chain 'R' and resid 158 through 166
      removed outlier: 3.558A  pdb=" N   ALA R 162 " --> pdb=" O   ARG R 158 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 167 through 186
    Processing helix  chain 'R' and resid 187 through 192
    Processing helix  chain 'R' and resid 211 through 227
    Processing helix  chain 'R' and resid 227 through 248
    Processing helix  chain 'R' and resid 327 through 360
      removed outlier: 4.132A  pdb=" N   ARG R 333 " --> pdb=" O   LYS R 329 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   MET R 334 " --> pdb=" O   ARG R 330 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   VAL R 339 " --> pdb=" O   LEU R 335 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   PHE R 342 " --> pdb=" O   ILE R 338 " (cutoff:3.500A)
      Proline residue:  R 348  - end of helix
    Processing helix  chain 'R' and resid 362 through 367
      removed outlier: 3.725A  pdb=" N   ALA R 366 " --> pdb=" O   GLY R 362 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU R 367 " --> pdb=" O   ALA R 363 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 362 through 367'
    Processing helix  chain 'R' and resid 369 through 391
      removed outlier: 4.091A  pdb=" N   LEU R 377 " --> pdb=" O   SER R 373 " (cutoff:3.500A)
      Proline residue:  R 387  - end of helix
      removed outlier: 3.678A  pdb=" N   TYR R 390 " --> pdb=" O   ASN R 386 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   CYS R 391 " --> pdb=" O   PRO R 387 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 394 through 405
      removed outlier: 3.837A  pdb=" N   ARG R 398 " --> pdb=" O   HIS R 394 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 192
    Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 227
      removed outlier: 5.613A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   ILE A 265 " --> pdb=" O   TYR A 321 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   HIS A 323 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   LEU A 267 " --> pdb=" O   HIS A 323 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.517A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.894A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105
      removed outlier: 5.898A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.135A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.098A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.405A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.995A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 276
    Processing sheet with id=AB1, first strand: chain 'B' and resid 295 through 296
      removed outlier: 3.677A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 197 through 198
      removed outlier: 3.699A  pdb=" N   VAL R 202 " --> pdb=" O   VAL R 198 " (cutoff:3.500A)

    321 hydrogen bonds defined for protein.
    942 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: 0.82

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1238
        1.33 -     1.45: 1708
        1.45 -     1.57: 3720
        1.57 -     1.70: 0
        1.70 -     1.82: 77
  Bond restraints: 6743
  Sorted by residual:
  bond pdb=" N   LEU A 284 "
       pdb=" CA  LEU A 284 "
    ideal  model  delta    sigma   weight residual
    1.458  1.500 -0.041 1.37e-02 5.33e+03 9.10e+00
  bond pdb=" C   ALA R 370 "
       pdb=" N   PRO R 371 "
    ideal  model  delta    sigma   weight residual
    1.334  1.399 -0.065 2.34e-02 1.83e+03 7.66e+00
  bond pdb=" N   MET R 134 "
       pdb=" CA  MET R 134 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.17e-02 7.31e+03 6.42e+00
  bond pdb=" CA  ASP B 291 "
       pdb=" C   ASP B 291 "
    ideal  model  delta    sigma   weight residual
    1.523  1.548 -0.025 1.34e-02 5.57e+03 3.48e+00
  bond pdb=" C   TYR R 189 "
       pdb=" N   PRO R 190 "
    ideal  model  delta    sigma   weight residual
    1.336  1.352 -0.016 9.80e-03 1.04e+04 2.83e+00
  ... (remaining 6738 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 8787
        1.98 -     3.96: 291
        3.96 -     5.95: 57
        5.95 -     7.93: 9
        7.93 -     9.91: 6
  Bond angle restraints: 9150
  Sorted by residual:
  angle pdb=" N   PCA E   1 "
        pdb=" CA  PCA E   1 "
        pdb=" CB  PCA E   1 "
      ideal   model   delta    sigma   weight residual
     110.50  102.21    8.29 1.70e+00 3.46e-01 2.38e+01
  angle pdb=" N   PRO E   3 "
        pdb=" CA  PRO E   3 "
        pdb=" C   PRO E   3 "
      ideal   model   delta    sigma   weight residual
     112.47  104.67    7.80 2.06e+00 2.36e-01 1.43e+01
  angle pdb=" CB  MET A  18 "
        pdb=" CG  MET A  18 "
        pdb=" SD  MET A  18 "
      ideal   model   delta    sigma   weight residual
     112.70  122.52   -9.82 3.00e+00 1.11e-01 1.07e+01
  angle pdb=" C   MET R 134 "
        pdb=" CA  MET R 134 "
        pdb=" CB  MET R 134 "
      ideal   model   delta    sigma   weight residual
     110.96  106.03    4.93 1.54e+00 4.22e-01 1.02e+01
  angle pdb=" CA  MET R 108 "
        pdb=" CB  MET R 108 "
        pdb=" CG  MET R 108 "
      ideal   model   delta    sigma   weight residual
     114.10  120.15   -6.05 2.00e+00 2.50e-01 9.14e+00
  ... (remaining 9145 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 3600
       17.86 -    35.72: 308
       35.72 -    53.58: 61
       53.58 -    71.44: 9
       71.44 -    89.30: 6
  Dihedral angle restraints: 3984
    sinusoidal: 1526
      harmonic: 2458
  Sorted by residual:
  dihedral pdb=" CB  CYS R 127 "
           pdb=" SG  CYS R 127 "
           pdb=" SG  CYS R 205 "
           pdb=" CB  CYS R 205 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  175.61  -82.61     1      1.00e+01 1.00e-02 8.37e+01
  dihedral pdb=" CA  CYS R 107 "
           pdb=" C   CYS R 107 "
           pdb=" N   MET R 108 "
           pdb=" CA  MET R 108 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.49  -20.51     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  MET R 186 "
           pdb=" C   MET R 186 "
           pdb=" N   VAL R 187 "
           pdb=" CA  VAL R 187 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.39   19.61     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 3981 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 779
       0.054 -    0.108: 218
       0.108 -    0.161: 52
       0.161 -    0.215: 4
       0.215 -    0.269: 4
  Chirality restraints: 1057
  Sorted by residual:
  chirality pdb=" CA  MET R 108 "
            pdb=" N   MET R 108 "
            pdb=" C   MET R 108 "
            pdb=" CB  MET R 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CA  MET R 134 "
            pdb=" N   MET R 134 "
            pdb=" C   MET R 134 "
            pdb=" CB  MET R 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CB  THR R 178 "
            pdb=" CA  THR R 178 "
            pdb=" OG1 THR R 178 "
            pdb=" CG2 THR R 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 1054 not shown)

  Planarity restraints: 1147
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" N   PCA E   1 "   -0.136 2.00e-02 2.50e+03   9.12e-02 1.04e+02
        pdb=" CA  PCA E   1 "    0.115 2.00e-02 2.50e+03
        pdb=" CG  PCA E   1 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD  PCA E   1 "   -0.024 2.00e-02 2.50e+03
        pdb=" OE  PCA E   1 "    0.087 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 288 "    0.044 5.00e-02 4.00e+02   6.70e-02 7.18e+00
        pdb=" N   PRO A 289 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 289 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 289 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C  52 "    0.044 5.00e-02 4.00e+02   6.63e-02 7.03e+00
        pdb=" N   PRO C  53 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO C  53 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO C  53 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1144 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1360
        2.78 -     3.31: 6306
        3.31 -     3.84: 11190
        3.84 -     4.37: 13216
        4.37 -     4.90: 22806
  Nonbonded interactions: 54878
  Sorted by model distance:
  nonbonded pdb=" O   HIS R 364 "
            pdb=" OG  SER R 368 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OG1 THR B  65 "
            pdb=" O   PRO B 107 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OE1 GLN B 176 "
            pdb=" OG1 THR B 179 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   MET B 325 "
            pdb=" ND2 ASN B 340 "
     model   vdw
     2.310 3.120
  ... (remaining 54873 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.00 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:             1.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.650
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6272
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      :  0.005   0.068   6744  Z= 0.226
  Angle     :  0.873   9.912   9152  Z= 0.468
  Chirality :  0.054   0.269   1057
  Planarity :  0.007   0.091   1147
  Dihedral  : 14.097  89.299   2389
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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 are not related in a simple way.
  whole: -1.49 (0.26), residues: 832
  helix: -0.08 (0.27), residues: 331
  sheet: -1.03 (0.41), residues: 131
  loop : -1.78 (0.28), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 398 
 TYR   0.016   0.003   TYR A 231 
 PHE   0.026   0.002   PHE R 343 
 TRP   0.036   0.003   TRP B 211 
 HIS   0.013   0.002   HIS A 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 6743)
  covalent geometry    : angle       0.87286 ( 9150)
  SS BOND              : bond        0.00541 (    1)
  SS BOND              : angle       1.94450 (    2)
  hydrogen bonds       : bond        0.14800 (  321)
  hydrogen bonds       : angle       7.45076 (  942)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: B  118 ASP cc_start: 0.7171 (t0) cc_final: 0.6889 (t0)
REVERT: C   32 LYS cc_start: 0.7713 (mppt) cc_final: 0.7474 (mtmm)
REVERT: E    5 LEU cc_start: 0.5831 (pt) cc_final: 0.5492 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0810
  time to fit residues: 13.4351
Evaluate side-chains
  100 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0570
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 115 ASN
R 204 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.193555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.166474 restraints weight = 7442.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.4246 rms_B_bonded: 2.06
r_work: 0.4075 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.4075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6535
moved from start:          0.1327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6744  Z= 0.145
  Angle     :  0.603   8.930   9152  Z= 0.316
  Chirality :  0.043   0.170   1057
  Planarity :  0.005   0.050   1147
  Dihedral  :  4.825  18.258    915
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  :  8.29 %
    Favored  : 90.45 %
  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 are not related in a simple way.
  whole: -0.85 (0.27), residues: 832
  helix:  0.73 (0.28), residues: 332
  sheet: -0.88 (0.40), residues: 142
  loop : -1.66 (0.29), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 152 
 TYR   0.018   0.002   TYR A 231 
 PHE   0.013   0.002   PHE B 234 
 TRP   0.014   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6743)
  covalent geometry    : angle       0.60278 ( 9150)
  SS BOND              : bond        0.00248 (    1)
  SS BOND              : angle       0.35344 (    2)
  hydrogen bonds       : bond        0.04448 (  321)
  hydrogen bonds       : angle       5.79352 (  942)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.7142 (mmm) cc_final: 0.6906 (mmm)
REVERT: A  276 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6797 (pm20)
REVERT: B  291 ASP cc_start: 0.5662 (t0) cc_final: 0.5286 (t0)
  outliers start: 9
  outliers final: 8
  residues processed: 111
  average time/residue: 0.0743
  time to fit residues: 11.5040
Evaluate side-chains
  105 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   67 MET
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  216 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 58 optimal weight:    0.5980
   chunk 80 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0870
   chunk 71 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0970
   overall best weight:    0.4156

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4470 r_free = 0.4470 target = 0.192810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.167098 restraints weight = 7293.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.4257 rms_B_bonded: 1.89
r_work: 0.4086 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.4086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6500
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6744  Z= 0.118
  Angle     :  0.554   7.587   9152  Z= 0.289
  Chirality :  0.042   0.162   1057
  Planarity :  0.004   0.043   1147
  Dihedral  :  4.571  23.053    915
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 10.25 %
    Favored  : 87.64 %
  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 are not related in a simple way.
  whole: -0.62 (0.28), residues: 832
  helix:  1.06 (0.29), residues: 331
  sheet: -0.97 (0.40), residues: 142
  loop : -1.57 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 152 
 TYR   0.014   0.001   TYR R 238 
 PHE   0.011   0.001   PHE R 110 
 TRP   0.015   0.002   TRP R 165 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6743)
  covalent geometry    : angle       0.55378 ( 9150)
  SS BOND              : bond        0.00073 (    1)
  SS BOND              : angle       0.05585 (    2)
  hydrogen bonds       : bond        0.04049 (  321)
  hydrogen bonds       : angle       5.46540 (  942)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.7179 (mmm) cc_final: 0.6931 (mmm)
REVERT: A  200 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.7223 (m-10)
REVERT: A  276 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6854 (pm20)
REVERT: B   61 MET cc_start: 0.6812 (ppp) cc_final: 0.6252 (ppp)
REVERT: B  270 ILE cc_start: 0.6545 (mm) cc_final: 0.6206 (mt)
  outliers start: 15
  outliers final: 12
  residues processed: 110
  average time/residue: 0.0704
  time to fit residues: 11.0246
Evaluate side-chains
  106 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   67 MET
Chi-restraints excluded: chain R residue  108 MET
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  216 GLN
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  393 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   chunk 58 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 54 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 196 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.187563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.162001 restraints weight = 7424.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.4215 rms_B_bonded: 1.90
r_work: 0.4024 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.4024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6610
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6744  Z= 0.151
  Angle     :  0.585   7.535   9152  Z= 0.304
  Chirality :  0.043   0.157   1057
  Planarity :  0.004   0.040   1147
  Dihedral  :  4.726  26.545    915
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 12.78 %
    Favored  : 84.55 %
  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 are not related in a simple way.
  whole: -0.69 (0.28), residues: 832
  helix:  1.08 (0.29), residues: 330
  sheet: -1.23 (0.40), residues: 142
  loop : -1.58 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R  57 
 TYR   0.014   0.002   TYR R 238 
 PHE   0.015   0.002   PHE B 234 
 TRP   0.013   0.002   TRP B 169 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6743)
  covalent geometry    : angle       0.58508 ( 9150)
  SS BOND              : bond        0.00143 (    1)
  SS BOND              : angle       0.31537 (    2)
  hydrogen bonds       : bond        0.04066 (  321)
  hydrogen bonds       : angle       5.49340 (  942)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
REVERT: A  200 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7577 (m-10)
REVERT: A  244 MET cc_start: 0.6001 (OUTLIER) cc_final: 0.5316 (mmm)
REVERT: A  248 MET cc_start: 0.6657 (OUTLIER) cc_final: 0.5660 (mtp)
REVERT: A  276 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6890 (pm20)
REVERT: B  270 ILE cc_start: 0.6667 (mm) cc_final: 0.6321 (mt)
REVERT: B  291 ASP cc_start: 0.6132 (t0) cc_final: 0.5806 (t0)
REVERT: R  134 MET cc_start: 0.5083 (mmp) cc_final: 0.4776 (mmp)
REVERT: R  246 TYR cc_start: 0.4940 (m-10) cc_final: 0.4711 (m-10)
  outliers start: 19
  outliers final: 12
  residues processed: 109
  average time/residue: 0.0674
  time to fit residues: 10.3016
Evaluate side-chains
  108 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   67 MET
Chi-restraints excluded: chain R residue  108 MET
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  216 GLN
Chi-restraints excluded: chain R residue  222 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 70 optimal weight:    0.3980
   chunk 76 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0970
   chunk 40 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0980
   chunk 22 optimal weight:    0.1980
   chunk 12 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.2778

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

Flipped N/Q/H residues before XYZ refinement:
A 196 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.199590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.171826 restraints weight = 7090.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.4275 rms_B_bonded: 2.06
r_work: 0.4127 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3963 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6553
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6744  Z= 0.107
  Angle     :  0.541   6.904   9152  Z= 0.280
  Chirality :  0.041   0.144   1057
  Planarity :  0.004   0.039   1147
  Dihedral  :  4.480  25.608    915
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 13.76 %
    Favored  : 83.85 %
  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 are not related in a simple way.
  whole: -0.42 (0.29), residues: 832
  helix:  1.30 (0.29), residues: 331
  sheet: -1.03 (0.39), residues: 148
  loop : -1.46 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 243 
 TYR   0.009   0.001   TYR R 238 
 PHE   0.026   0.001   PHE B 292 
 TRP   0.019   0.002   TRP B 169 
 HIS   0.002   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 6743)
  covalent geometry    : angle       0.54065 ( 9150)
  SS BOND              : bond        0.00019 (    1)
  SS BOND              : angle       0.04101 (    2)
  hydrogen bonds       : bond        0.03655 (  321)
  hydrogen bonds       : angle       5.24228 (  942)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.7202 (m-10)
REVERT: A  248 MET cc_start: 0.6665 (OUTLIER) cc_final: 0.5833 (mtp)
REVERT: A  276 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6957 (pm20)
REVERT: B   61 MET cc_start: 0.6823 (ppp) cc_final: 0.6507 (ppp)
REVERT: B  270 ILE cc_start: 0.6534 (mm) cc_final: 0.6241 (mt)
REVERT: R  353 ASN cc_start: 0.7179 (m-40) cc_final: 0.6773 (m110)
  outliers start: 17
  outliers final: 11
  residues processed: 118
  average time/residue: 0.0675
  time to fit residues: 11.2606
Evaluate side-chains
  111 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   67 MET
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  216 GLN
Chi-restraints excluded: chain R residue  222 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 71 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 73 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9980
   chunk 63 optimal weight:    0.5980
   chunk 68 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 196 HIS
A 332 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.196133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.167647 restraints weight = 7115.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.4231 rms_B_bonded: 2.12
r_work: 0.4084 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3918 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6621
moved from start:          0.2163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6744  Z= 0.136
  Angle     :  0.579  11.339   9152  Z= 0.295
  Chirality :  0.042   0.152   1057
  Planarity :  0.004   0.040   1147
  Dihedral  :  4.566  28.363    915
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 15.45 %
    Favored  : 82.16 %
  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 are not related in a simple way.
  whole: -0.48 (0.29), residues: 832
  helix:  1.31 (0.29), residues: 331
  sheet: -1.08 (0.39), residues: 148
  loop : -1.55 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 152 
 TYR   0.010   0.001   TYR R 238 
 PHE   0.021   0.002   PHE B 199 
 TRP   0.019   0.002   TRP R 165 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6743)
  covalent geometry    : angle       0.57920 ( 9150)
  SS BOND              : bond        0.00139 (    1)
  SS BOND              : angle       0.29141 (    2)
  hydrogen bonds       : bond        0.03800 (  321)
  hydrogen bonds       : angle       5.30944 (  942)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 PHE cc_start: 0.7702 (OUTLIER) cc_final: 0.7447 (m-80)
REVERT: A  248 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6049 (mtp)
REVERT: A  276 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6973 (pm20)
REVERT: B  270 ILE cc_start: 0.6353 (mm) cc_final: 0.6083 (mt)
REVERT: R  246 TYR cc_start: 0.4937 (m-10) cc_final: 0.4625 (m-10)
REVERT: R  353 ASN cc_start: 0.7233 (m-40) cc_final: 0.6813 (m110)
  outliers start: 17
  outliers final: 12
  residues processed: 109
  average time/residue: 0.0709
  time to fit residues: 10.9954
Evaluate side-chains
  112 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   67 MET
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  216 GLN
Chi-restraints excluded: chain R residue  222 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 60 optimal weight:    0.5980
   chunk 14 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 79 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9980
   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 196 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.194786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.166762 restraints weight = 7076.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.4223 rms_B_bonded: 2.07
r_work: 0.4073 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3906 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6638
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6744  Z= 0.144
  Angle     :  0.584   9.761   9152  Z= 0.299
  Chirality :  0.043   0.175   1057
  Planarity :  0.004   0.041   1147
  Dihedral  :  4.641  30.177    915
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 15.03 %
    Favored  : 82.02 %
  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 are not related in a simple way.
  whole: -0.57 (0.28), residues: 832
  helix:  1.21 (0.29), residues: 331
  sheet: -1.10 (0.40), residues: 148
  loop : -1.58 (0.30), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 152 
 TYR   0.011   0.001   TYR R 238 
 PHE   0.026   0.002   PHE A 275 
 TRP   0.015   0.002   TRP R 165 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 6743)
  covalent geometry    : angle       0.58387 ( 9150)
  SS BOND              : bond        0.00145 (    1)
  SS BOND              : angle       0.30245 (    2)
  hydrogen bonds       : bond        0.03864 (  321)
  hydrogen bonds       : angle       5.34685 (  942)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.5986 (mtp)
REVERT: A  275 PHE cc_start: 0.6811 (t80) cc_final: 0.6567 (t80)
REVERT: B   61 MET cc_start: 0.6830 (ppp) cc_final: 0.6435 (ppp)
REVERT: B  270 ILE cc_start: 0.6429 (mm) cc_final: 0.6167 (mt)
REVERT: R  246 TYR cc_start: 0.4966 (m-10) cc_final: 0.4680 (m-10)
REVERT: R  353 ASN cc_start: 0.7278 (m-40) cc_final: 0.6884 (m110)
  outliers start: 21
  outliers final: 18
  residues processed: 109
  average time/residue: 0.0721
  time to fit residues: 11.0523
Evaluate side-chains
  114 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   44 HIS
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   67 MET
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  216 GLN
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  331 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 73 optimal weight:    0.6980
   chunk 68 optimal weight:    0.4980
   chunk 60 optimal weight:    0.7980
   chunk 81 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 196 HIS
A 332 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.192119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.162740 restraints weight = 7087.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.4221 rms_B_bonded: 2.19
r_work: 0.4072 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6486
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6744  Z= 0.134
  Angle     :  0.583   9.600   9152  Z= 0.296
  Chirality :  0.042   0.169   1057
  Planarity :  0.004   0.042   1147
  Dihedral  :  4.622  32.914    915
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 15.31 %
    Favored  : 81.60 %
  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 are not related in a simple way.
  whole: -0.54 (0.28), residues: 832
  helix:  1.24 (0.29), residues: 331
  sheet: -1.07 (0.40), residues: 148
  loop : -1.60 (0.30), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 152 
 TYR   0.010   0.001   TYR R 238 
 PHE   0.021   0.002   PHE B 199 
 TRP   0.017   0.002   TRP R 165 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 6743)
  covalent geometry    : angle       0.58321 ( 9150)
  SS BOND              : bond        0.00119 (    1)
  SS BOND              : angle       0.23818 (    2)
  hydrogen bonds       : bond        0.03797 (  321)
  hydrogen bonds       : angle       5.29258 (  942)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.5837 (mtp)
REVERT: A  276 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6877 (pm20)
REVERT: B   61 MET cc_start: 0.6757 (ppp) cc_final: 0.6367 (ppp)
REVERT: B  270 ILE cc_start: 0.6533 (mm) cc_final: 0.6265 (mt)
REVERT: R  246 TYR cc_start: 0.4921 (m-10) cc_final: 0.4626 (m-10)
REVERT: R  353 ASN cc_start: 0.7130 (m-40) cc_final: 0.6860 (m110)
  outliers start: 22
  outliers final: 17
  residues processed: 110
  average time/residue: 0.0712
  time to fit residues: 11.0779
Evaluate side-chains
  111 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   67 MET
Chi-restraints excluded: chain R residue  108 MET
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  216 GLN
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  331 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 36 optimal weight:    0.4980
   chunk 59 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 80 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 196 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4470 r_free = 0.4470 target = 0.192328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.163063 restraints weight = 7130.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.4222 rms_B_bonded: 2.19
r_work: 0.4069 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.4069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6487
moved from start:          0.2424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6744  Z= 0.134
  Angle     :  0.587   9.320   9152  Z= 0.298
  Chirality :  0.043   0.153   1057
  Planarity :  0.004   0.042   1147
  Dihedral  :  4.642  33.937    915
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 15.87 %
    Favored  : 81.32 %
  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 are not related in a simple way.
  whole: -0.61 (0.28), residues: 832
  helix:  1.14 (0.29), residues: 337
  sheet: -1.09 (0.40), residues: 148
  loop : -1.64 (0.30), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 152 
 TYR   0.010   0.001   TYR R 238 
 PHE   0.022   0.002   PHE B 199 
 TRP   0.023   0.002   TRP R 165 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6743)
  covalent geometry    : angle       0.58707 ( 9150)
  SS BOND              : bond        0.00100 (    1)
  SS BOND              : angle       0.24263 (    2)
  hydrogen bonds       : bond        0.03812 (  321)
  hydrogen bonds       : angle       5.30510 (  942)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.5857 (mtp)
REVERT: A  276 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6968 (pm20)
REVERT: B   61 MET cc_start: 0.6855 (ppp) cc_final: 0.6420 (ppp)
REVERT: B  270 ILE cc_start: 0.6461 (mm) cc_final: 0.6193 (mt)
REVERT: R  134 MET cc_start: 0.4898 (mmp) cc_final: 0.4680 (mmp)
REVERT: R  246 TYR cc_start: 0.4928 (m-10) cc_final: 0.4634 (m-10)
  outliers start: 20
  outliers final: 18
  residues processed: 109
  average time/residue: 0.0709
  time to fit residues: 10.9661
Evaluate side-chains
  116 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   44 HIS
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   67 MET
Chi-restraints excluded: chain R residue  108 MET
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  216 GLN
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  331 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 39 optimal weight:    0.1980
   chunk 81 optimal weight:    0.8980
   chunk 61 optimal weight:    0.4980
   chunk 41 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 5 optimal weight:    0.4980
   chunk 27 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 196 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.193062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.164054 restraints weight = 7076.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.4234 rms_B_bonded: 2.17
r_work: 0.4081 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.4081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6469
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6744  Z= 0.126
  Angle     :  0.591   9.204   9152  Z= 0.300
  Chirality :  0.042   0.148   1057
  Planarity :  0.004   0.042   1147
  Dihedral  :  4.620  35.206    915
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 16.71 %
    Favored  : 80.76 %
  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 are not related in a simple way.
  whole: -0.58 (0.28), residues: 832
  helix:  1.15 (0.29), residues: 337
  sheet: -1.09 (0.40), residues: 148
  loop : -1.61 (0.30), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 152 
 TYR   0.009   0.001   TYR R 238 
 PHE   0.023   0.002   PHE B 199 
 TRP   0.022   0.002   TRP R 165 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6743)
  covalent geometry    : angle       0.59153 ( 9150)
  SS BOND              : bond        0.00054 (    1)
  SS BOND              : angle       0.22422 (    2)
  hydrogen bonds       : bond        0.03736 (  321)
  hydrogen bonds       : angle       5.30317 (  942)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 MET cc_start: 0.6627 (OUTLIER) cc_final: 0.5826 (mtp)
REVERT: A  276 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6959 (pm20)
REVERT: B   61 MET cc_start: 0.6808 (ppp) cc_final: 0.6402 (ppp)
REVERT: B  270 ILE cc_start: 0.6406 (mm) cc_final: 0.6183 (mt)
REVERT: R  134 MET cc_start: 0.4855 (mmp) cc_final: 0.4655 (mmp)
REVERT: R  246 TYR cc_start: 0.4935 (m-10) cc_final: 0.4644 (m-10)
  outliers start: 18
  outliers final: 16
  residues processed: 109
  average time/residue: 0.0672
  time to fit residues: 10.2484
Evaluate side-chains
  115 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   67 MET
Chi-restraints excluded: chain R residue  108 MET
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  216 GLN
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  331 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0470
   chunk 73 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
A 196 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.196540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.168747 restraints weight = 7109.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.4245 rms_B_bonded: 2.08
r_work: 0.4091 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3930 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6613
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6744  Z= 0.127
  Angle     :  0.592   8.956   9152  Z= 0.302
  Chirality :  0.042   0.143   1057
  Planarity :  0.004   0.042   1147
  Dihedral  :  4.606  36.643    915
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 16.85 %
    Favored  : 80.48 %
  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 are not related in a simple way.
  whole: -0.63 (0.28), residues: 832
  helix:  1.10 (0.29), residues: 339
  sheet: -1.09 (0.40), residues: 148
  loop : -1.64 (0.30), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 219 
 TYR   0.011   0.001   TYR R 238 
 PHE   0.023   0.002   PHE B 199 
 TRP   0.025   0.002   TRP R 346 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6743)
  covalent geometry    : angle       0.59206 ( 9150)
  SS BOND              : bond        0.00073 (    1)
  SS BOND              : angle       0.24202 (    2)
  hydrogen bonds       : bond        0.03742 (  321)
  hydrogen bonds       : angle       5.33292 (  942)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2008.73 seconds
wall clock time: 35 minutes 5.99 seconds (2105.99 seconds total)