Starting phenix.real_space_refine
on Wed Aug  5 08:59:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/24xb_69886/08_2026/24xb_69886.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/24xb_69886/08_2026/24xb_69886.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/24xb_69886/08_2026/24xb_69886.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/24xb_69886/08_2026/24xb_69886.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/24xb_69886/08_2026/24xb_69886.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/24xb_69886/08_2026/24xb_69886.map"
  }
  resolution = 2.65
  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=  -0.001 sd=   0.012
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      56      5.16       5
     C    5650      2.51       5
     N    1511      2.21       5
     O    1620      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8837
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2559
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2559
          Classifications: {'peptide': 333}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 327}
    Chain: "C"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 418
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
    Chain: "D"
      Number of atoms: 1777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1777
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1798
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 5, 'TRANS': 212}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 2285
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2285
          Classifications: {'peptide': 287}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 11, 'TRANS': 275}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 2.11, per 1000 atoms: 0.24
  Number of scatterers: 8837
  At special positions: 0
  Unit cell: (89.64, 119.52, 126.16, 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      56     16.00
     O    1620      8.00
     N    1511      7.00
     C    5650      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  39 " - pdb=" SG  CYS D 113 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 111 " - pdb=" SG  CYS A 194 " 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 474.0 milliseconds
  

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2114

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 14 sheets defined
      34.9% alpha, 20.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 10 through 24
      removed outlier: 3.805A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'D' and resid 45 through 49
    Processing helix  chain 'D' and resid 79 through 82
      removed outlier: 3.740A  pdb=" N   LYS D  82 " --> pdb=" O   ASP D  79 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 79 through 82'
    Processing helix  chain 'E' and resid 6 through 30
    Processing helix  chain 'E' and resid 45 through 57
    Processing helix  chain 'E' and resid 206 through 215
      removed outlier: 3.522A  pdb=" N   LYS E 209 " --> pdb=" O   GLU E 206 " (cutoff:3.500A)
      removed outlier: 5.184A  pdb=" N   ILE E 211 " --> pdb=" O   ARG E 208 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   HIS E 212 " --> pdb=" O   LYS E 209 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 242 through 247
    Processing helix  chain 'E' and resid 269 through 277
    Processing helix  chain 'E' and resid 297 through 309
    Processing helix  chain 'E' and resid 329 through 350
    Processing helix  chain 'A' and resid 38 through 66
    Processing helix  chain 'A' and resid 77 through 102
      removed outlier: 3.590A  pdb=" N   LEU A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE A  82 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   LEU A  87 " --> pdb=" O   CYS A  83 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   PHE A  88 " --> pdb=" O   ALA A  84 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ILE A  89 " --> pdb=" O   ASP A  85 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ILE A  92 " --> pdb=" O   PHE A  88 " (cutoff:3.500A)
      Proline residue:  A  93  - end of helix
    Processing helix  chain 'A' and resid 109 through 142
      removed outlier: 4.230A  pdb=" N   PHE A 115 " --> pdb=" O   CYS A 111 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   TYR A 116 " --> pdb=" O   HIS A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 170
    Processing helix  chain 'A' and resid 171 through 176
    Processing helix  chain 'A' and resid 200 through 244
      removed outlier: 4.325A  pdb=" N   VAL A 218 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      Proline residue:  A 219  - end of helix
      removed outlier: 3.698A  pdb=" N   SER A 244 " --> pdb=" O   ARG A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 277
      removed outlier: 3.698A  pdb=" N   PHE A 273 " --> pdb=" O   LEU A 269 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   PHE A 274 " --> pdb=" O   MET A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 293
      removed outlier: 4.182A  pdb=" N   ILE A 281 " --> pdb=" O   TRP A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 312
      removed outlier: 3.559A  pdb=" N   PHE A 304 " --> pdb=" O   PRO A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 323
      Proline residue:  A 318  - end of helix
      removed outlier: 3.542A  pdb=" N   MET A 323 " --> pdb=" O   ILE A 319 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.517A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.919A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.380A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.851A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.386A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.489A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.031A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.371A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 23 through 24
      removed outlier: 5.754A  pdb=" N   GLY D  33 " --> pdb=" O   SER D 102 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 27 through 29
      removed outlier: 6.187A  pdb=" N   GLY D  27 " --> pdb=" O   THR D 135 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 75 through 77
      removed outlier: 4.311A  pdb=" N   PHE D 127 " --> pdb=" O   ARG D 115 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 157 through 158
    Processing sheet with id=AB3, first strand: chain 'D' and resid 211 through 212
      removed outlier: 6.569A  pdb=" N   TRP D 193 " --> pdb=" O   LEU D 205 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   TYR D 207 " --> pdb=" O   LEU D 191 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   LEU D 191 " --> pdb=" O   TYR D 207 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 184 through 189
      removed outlier: 3.529A  pdb=" N   ILE E 184 " --> pdb=" O   ASP E 199 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   MET E 197 " --> pdb=" O   TYR E 186 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   PHE E 188 " --> pdb=" O   PHE E 195 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   LEU E  36 " --> pdb=" O   VAL E 198 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   SER E 219 " --> pdb=" O   LYS E  35 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   ILE E 220 " --> pdb=" O   ILE E 264 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   PHE E 266 " --> pdb=" O   ILE E 220 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 184 through 189
      removed outlier: 3.529A  pdb=" N   ILE E 184 " --> pdb=" O   ASP E 199 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   MET E 197 " --> pdb=" O   TYR E 186 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   PHE E 188 " --> pdb=" O   PHE E 195 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   LEU E  36 " --> pdb=" O   VAL E 198 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   SER E 219 " --> pdb=" O   LYS E  35 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   ILE E 220 " --> pdb=" O   ILE E 264 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   PHE E 266 " --> pdb=" O   ILE E 220 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   THR E 323 " --> pdb=" O   LEU E 267 " (cutoff:3.500A)

    400 hydrogen bonds defined for protein.
    1131 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: 1.57

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2845
        1.34 -     1.46: 2068
        1.46 -     1.58: 4022
        1.58 -     1.70: 0
        1.70 -     1.81: 83
  Bond restraints: 9018
  Sorted by residual:
  bond pdb=" C   ILE A  92 "
       pdb=" N   PRO A  93 "
    ideal  model  delta    sigma   weight residual
    1.335  1.362 -0.027 1.36e-02 5.41e+03 3.82e+00
  bond pdb=" N   GLU A 204 "
       pdb=" CA  GLU A 204 "
    ideal  model  delta    sigma   weight residual
    1.459  1.446  0.013 1.19e-02 7.06e+03 1.21e+00
  bond pdb=" C   GLY A 203 "
       pdb=" N   GLU A 204 "
    ideal  model  delta    sigma   weight residual
    1.334  1.322  0.013 1.27e-02 6.20e+03 9.81e-01
  bond pdb=" C   ILE A 201 "
       pdb=" N   PRO A 202 "
    ideal  model  delta    sigma   weight residual
    1.335  1.347 -0.011 1.36e-02 5.41e+03 7.12e-01
  bond pdb=" CB  PRO D 253 "
       pdb=" CG  PRO D 253 "
    ideal  model  delta    sigma   weight residual
    1.506  1.475  0.031 3.90e-02 6.57e+02 6.52e-01
  ... (remaining 9013 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 12049
        2.29 -     4.58: 146
        4.58 -     6.87: 21
        6.87 -     9.17: 2
        9.17 -    11.46: 3
  Bond angle restraints: 12221
  Sorted by residual:
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     113.71  109.06    4.65 9.50e-01 1.11e+00 2.39e+01
  angle pdb=" C   TYR E 285 "
        pdb=" N   PHE E 286 "
        pdb=" CA  PHE E 286 "
      ideal   model   delta    sigma   weight residual
     121.80  133.26  -11.46 2.44e+00 1.68e-01 2.21e+01
  angle pdb=" CA  LEU A 196 "
        pdb=" CB  LEU A 196 "
        pdb=" CG  LEU A 196 "
      ideal   model   delta    sigma   weight residual
     116.30  127.37  -11.07 3.50e+00 8.16e-02 1.00e+01
  angle pdb=" C   ARG D 208 "
        pdb=" N   MET D 209 "
        pdb=" CA  MET D 209 "
      ideal   model   delta    sigma   weight residual
     121.54  127.44   -5.90 1.91e+00 2.74e-01 9.55e+00
  angle pdb=" N   GLU D 106 "
        pdb=" CA  GLU D 106 "
        pdb=" C   GLU D 106 "
      ideal   model   delta    sigma   weight residual
     112.86  109.36    3.50 1.22e+00 6.72e-01 8.21e+00
  ... (remaining 12216 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.41: 4860
       17.41 -    34.81: 415
       34.81 -    52.22: 59
       52.22 -    69.63: 11
       69.63 -    87.03: 12
  Dihedral angle restraints: 5357
    sinusoidal: 2097
      harmonic: 3260
  Sorted by residual:
  dihedral pdb=" CA  MET A 276 "
           pdb=" C   MET A 276 "
           pdb=" N   TRP A 277 "
           pdb=" CA  TRP A 277 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.48   22.52     0      5.00e+00 4.00e-02 2.03e+01
  dihedral pdb=" CA  LYS E  27 "
           pdb=" C   LYS E  27 "
           pdb=" N   ARG E  28 "
           pdb=" CA  ARG E  28 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.12   20.88     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.85   19.15     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 5354 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1118
       0.052 -    0.103: 241
       0.103 -    0.155: 46
       0.155 -    0.206: 1
       0.206 -    0.258: 1
  Chirality restraints: 1407
  Sorted by residual:
  chirality pdb=" CG  LEU A 196 "
            pdb=" CB  LEU A 196 "
            pdb=" CD1 LEU A 196 "
            pdb=" CD2 LEU A 196 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.67e+00
  chirality pdb=" CB  THR E 323 "
            pdb=" CA  THR E 323 "
            pdb=" OG1 THR E 323 "
            pdb=" CG2 THR E 323 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.50e-01
  chirality pdb=" CA  ILE A 193 "
            pdb=" N   ILE A 193 "
            pdb=" C   ILE A 193 "
            pdb=" CB  ILE A 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.85e-01
  ... (remaining 1404 not shown)

  Planarity restraints: 1535
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D 164 "   -0.042 5.00e-02 4.00e+02   6.42e-02 6.60e+00
        pdb=" N   PRO D 165 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO D 165 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO D 165 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR E 186 "    0.032 5.00e-02 4.00e+02   4.81e-02 3.71e+00
        pdb=" N   PRO E 187 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO E 187 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO E 187 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B 205 "   -0.008 2.00e-02 2.50e+03   1.56e-02 2.43e+00
        pdb=" CG  ASP B 205 "    0.027 2.00e-02 2.50e+03
        pdb=" OD1 ASP B 205 "   -0.010 2.00e-02 2.50e+03
        pdb=" OD2 ASP B 205 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1532 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 330
        2.71 -     3.26: 9234
        3.26 -     3.81: 14716
        3.81 -     4.35: 18237
        4.35 -     4.90: 31147
  Nonbonded interactions: 73664
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OH  TYR D 192 "
            pdb=" OE2 GLU E   8 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OG1 THR B  29 "
            pdb=" OE1 GLN B  32 "
     model   vdw
     2.225 3.040
  ... (remaining 73659 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.570
  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:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.840
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
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      :  0.003   0.031   9020  Z= 0.133
  Angle     :  0.640  11.458  12225  Z= 0.330
  Chirality :  0.044   0.258   1407
  Planarity :  0.004   0.064   1535
  Dihedral  : 13.425  87.031   3237
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.04 (0.26), residues: 1097
  helix:  1.43 (0.28), residues: 375
  sheet: -0.33 (0.33), residues: 255
  loop : -0.89 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 104 
 TYR   0.016   0.001   TYR A 165 
 PHE   0.015   0.001   PHE B 234 
 TRP   0.015   0.001   TRP A 104 
 HIS   0.010   0.001   HIS A 142 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 ( 9018)
  covalent geometry    : angle       0.63972 /  0.33 (12221)
  SS BOND              : bond        0.00256 /  0.13 (    2)
  SS BOND              : angle       0.43976 /  0.22 (    4)
  hydrogen bonds       : bond        0.17102 / 11.57 (  396)
  hydrogen bonds       : angle       6.68516 /  4.78 ( 1131)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
REVERT: B   16 ASN cc_start: 0.8531 (m-40) cc_final: 0.8187 (m110)
REVERT: B   17 GLN cc_start: 0.9352 (tm-30) cc_final: 0.9072 (tm-30)
REVERT: C   22 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8686 (tm-30)
REVERT: D   60 LYS cc_start: 0.9271 (mptt) cc_final: 0.8884 (mmtp)
REVERT: D   63 GLU cc_start: 0.7801 (tt0) cc_final: 0.7560 (tt0)
REVERT: D   82 LYS cc_start: 0.9015 (tppt) cc_final: 0.8768 (tppp)
REVERT: D  211 ASN cc_start: 0.8598 (m110) cc_final: 0.8380 (m110)
REVERT: D  235 ARG cc_start: 0.8121 (mmp-170) cc_final: 0.7914 (mmp-170)
REVERT: E   35 LYS cc_start: 0.8608 (mtmm) cc_final: 0.8396 (mtmm)
REVERT: A  105 LEU cc_start: 0.7097 (mm) cc_final: 0.6841 (pt)
REVERT: A  258 GLN cc_start: 0.8551 (mm110) cc_final: 0.8222 (mm110)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.5836
  time to fit residues: 131.1732
Evaluate side-chains
  168 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  36 ASN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 ASN
D 159 GLN
D 186 ASN
E  22 GLN
** A  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 313 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.123464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.087025 restraints weight = 15872.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 3.49
r_work: 0.3133 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9020  Z= 0.177
  Angle     :  0.706  14.304  12225  Z= 0.350
  Chirality :  0.046   0.217   1407
  Planarity :  0.004   0.051   1535
  Dihedral  :  4.483  26.726   1216
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 15.17 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.02 (0.26), residues: 1097
  helix:  1.32 (0.27), residues: 380
  sheet: -0.09 (0.34), residues: 243
  loop : -1.05 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 196 
 TYR   0.015   0.001   TYR A 165 
 PHE   0.021   0.002   PHE A 311 
 TRP   0.015   0.001   TRP B 211 
 HIS   0.003   0.001   HIS E 281 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00405 /  0.18 ( 9018)
  covalent geometry    : angle       0.70638 /  0.35 (12221)
  SS BOND              : bond        0.00401 /  0.20 (    2)
  SS BOND              : angle       0.86807 /  0.46 (    4)
  hydrogen bonds       : bond        0.03990 /  2.66 (  396)
  hydrogen bonds       : angle       5.02230 /  3.55 ( 1131)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 184
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
REVERT: B   16 ASN cc_start: 0.8619 (m-40) cc_final: 0.8406 (m110)
REVERT: B   17 GLN cc_start: 0.9319 (tm-30) cc_final: 0.9011 (tm-30)
REVERT: B   44 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8308 (mp10)
REVERT: C   14 LYS cc_start: 0.9525 (OUTLIER) cc_final: 0.9275 (ttmt)
REVERT: C   22 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8705 (tm-30)
REVERT: D   60 LYS cc_start: 0.9319 (mptt) cc_final: 0.9049 (mmtp)
REVERT: D   63 GLU cc_start: 0.8537 (tt0) cc_final: 0.8213 (tt0)
REVERT: D   82 LYS cc_start: 0.8883 (tppt) cc_final: 0.8602 (tppp)
REVERT: D  177 ARG cc_start: 0.8246 (tpp-160) cc_final: 0.7929 (mmm160)
REVERT: D  211 ASN cc_start: 0.8090 (m110) cc_final: 0.7663 (m-40)
REVERT: D  235 ARG cc_start: 0.8510 (mmp-170) cc_final: 0.8087 (mmp-170)
REVERT: E   25 ARG cc_start: 0.7242 (tmm-80) cc_final: 0.6998 (tmm-80)
REVERT: E   28 ARG cc_start: 0.7297 (mmp80) cc_final: 0.7002 (mmm-85)
REVERT: E  250 ARG cc_start: 0.7997 (pmt-80) cc_final: 0.7737 (tmt-80)
REVERT: A  105 LEU cc_start: 0.7310 (mm) cc_final: 0.7050 (pt)
REVERT: A  275 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7876 (tp)
  outliers start: 19
  outliers final: 6
  residues processed: 190
  average time/residue: 0.5754
  time to fit residues: 116.2840
Evaluate side-chains
  172 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 164
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain C residue   14 LYS
Chi-restraints excluded: chain E residue   41 THR
Chi-restraints excluded: chain E residue  189 ASP
Chi-restraints excluded: chain A residue  133 SER
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  275 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 109 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 101 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0270
   chunk 1 optimal weight:    6.9990
   chunk 96 optimal weight:    7.9990
   chunk 77 optimal weight:    0.9990
   chunk 86 optimal weight:   20.0000
   chunk 65 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   overall best weight:    0.7438

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
E  52 GLN
** A  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 215 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.123834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.086844 restraints weight = 15678.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 3.49
r_work: 0.3126 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9020  Z= 0.144
  Angle     :  0.670  13.712  12225  Z= 0.333
  Chirality :  0.045   0.314   1407
  Planarity :  0.004   0.044   1535
  Dihedral  :  4.369  25.131   1216
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.44 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.11 (0.26), residues: 1097
  helix:  1.26 (0.27), residues: 374
  sheet: -0.21 (0.34), residues: 247
  loop : -1.04 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  19 
 TYR   0.018   0.001   TYR E 285 
 PHE   0.021   0.001   PHE A 311 
 TRP   0.016   0.001   TRP B 211 
 HIS   0.003   0.001   HIS A 142 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.14 ( 9018)
  covalent geometry    : angle       0.67011 /  0.33 (12221)
  SS BOND              : bond        0.00501 /  0.26 (    2)
  SS BOND              : angle       0.97516 /  0.51 (    4)
  hydrogen bonds       : bond        0.03614 /  2.44 (  396)
  hydrogen bonds       : angle       4.75991 /  3.37 ( 1131)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 176
  time to evaluate  : 0.370 
Fit side-chains
REVERT: B   16 ASN cc_start: 0.8639 (m-40) cc_final: 0.8328 (m110)
REVERT: B   17 GLN cc_start: 0.9323 (tm-30) cc_final: 0.9031 (tm-30)
REVERT: B   44 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8272 (mp10)
REVERT: B   96 ARG cc_start: 0.8992 (ttm110) cc_final: 0.8668 (ttm110)
REVERT: B  217 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7691 (pmt)
REVERT: C   14 LYS cc_start: 0.9495 (OUTLIER) cc_final: 0.9246 (ttmt)
REVERT: C   22 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8584 (tm-30)
REVERT: D   60 LYS cc_start: 0.9296 (mptt) cc_final: 0.9048 (mmtp)
REVERT: D   63 GLU cc_start: 0.8469 (tt0) cc_final: 0.8176 (tt0)
REVERT: D   82 LYS cc_start: 0.8814 (tppt) cc_final: 0.8505 (tppp)
REVERT: D  104 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7260 (pmm-80)
REVERT: D  106 GLU cc_start: 0.8327 (pp20) cc_final: 0.8105 (pp20)
REVERT: D  177 ARG cc_start: 0.8209 (tpp-160) cc_final: 0.7868 (mmm160)
REVERT: D  211 ASN cc_start: 0.7963 (m110) cc_final: 0.7639 (m-40)
REVERT: D  235 ARG cc_start: 0.8538 (mmp-170) cc_final: 0.8134 (mmp-170)
REVERT: E   18 MET cc_start: 0.7810 (tpt) cc_final: 0.7280 (tpt)
REVERT: E   22 GLN cc_start: 0.8438 (mm-40) cc_final: 0.7987 (mm110)
REVERT: E   25 ARG cc_start: 0.7144 (tmm-80) cc_final: 0.6864 (tmm-80)
REVERT: E   28 ARG cc_start: 0.7275 (mmp80) cc_final: 0.6961 (mmm-85)
REVERT: E  228 GLU cc_start: 0.7525 (tp30) cc_final: 0.7160 (tp30)
REVERT: E  250 ARG cc_start: 0.7985 (pmt-80) cc_final: 0.7749 (tmt-80)
REVERT: E  306 MET cc_start: 0.9256 (mmm) cc_final: 0.9048 (mmm)
REVERT: A  275 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7898 (tp)
  outliers start: 27
  outliers final: 6
  residues processed: 189
  average time/residue: 0.6324
  time to fit residues: 126.7119
Evaluate side-chains
  176 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 166
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain C residue   14 LYS
Chi-restraints excluded: chain D residue  104 ARG
Chi-restraints excluded: chain E residue   41 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  133 SER
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  275 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 77 optimal weight:    5.9990
   chunk 86 optimal weight:    4.9990
   chunk 84 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 100 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 93 optimal weight:    0.0970
   overall best weight:    1.2186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 203 GLN
** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.122192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.084246 restraints weight = 15846.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 3.55
r_work: 0.3092 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9020  Z= 0.176
  Angle     :  0.675  13.916  12225  Z= 0.333
  Chirality :  0.045   0.207   1407
  Planarity :  0.004   0.042   1535
  Dihedral  :  4.377  23.446   1216
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 19.50 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.08 (0.26), residues: 1097
  helix:  1.29 (0.27), residues: 375
  sheet: -0.24 (0.32), residues: 264
  loop : -1.01 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 219 
 TYR   0.012   0.001   TYR D 207 
 PHE   0.014   0.001   PHE E 286 
 TRP   0.020   0.001   TRP A 104 
 HIS   0.003   0.001   HIS E 281 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00406 /  0.18 ( 9018)
  covalent geometry    : angle       0.67444 /  0.33 (12221)
  SS BOND              : bond        0.00373 /  0.19 (    2)
  SS BOND              : angle       0.92178 /  0.48 (    4)
  hydrogen bonds       : bond        0.03499 /  2.36 (  396)
  hydrogen bonds       : angle       4.60633 /  3.27 ( 1131)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 190
  time to evaluate  : 0.339 
Fit side-chains
REVERT: B   16 ASN cc_start: 0.8560 (m-40) cc_final: 0.8330 (m-40)
REVERT: B   17 GLN cc_start: 0.9344 (tm-30) cc_final: 0.9014 (pp30)
REVERT: B   96 ARG cc_start: 0.9007 (ttm110) cc_final: 0.8669 (ttm110)
REVERT: C   14 LYS cc_start: 0.9505 (OUTLIER) cc_final: 0.9248 (ttmt)
REVERT: C   22 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8717 (tm-30)
REVERT: D   59 GLU cc_start: 0.8487 (pp20) cc_final: 0.8276 (pp20)
REVERT: D   60 LYS cc_start: 0.9314 (mptt) cc_final: 0.9037 (mmtp)
REVERT: D   63 GLU cc_start: 0.8412 (tt0) cc_final: 0.8085 (tt0)
REVERT: D   82 LYS cc_start: 0.8841 (tppt) cc_final: 0.8535 (tppp)
REVERT: D  104 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7305 (pmm-80)
REVERT: D  106 GLU cc_start: 0.8450 (pp20) cc_final: 0.8143 (pp20)
REVERT: D  211 ASN cc_start: 0.7943 (m110) cc_final: 0.7740 (m-40)
REVERT: D  235 ARG cc_start: 0.8558 (mmp-170) cc_final: 0.8267 (mmp-170)
REVERT: E    8 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8470 (mt-10)
REVERT: E   18 MET cc_start: 0.7808 (tpt) cc_final: 0.7608 (tmm)
REVERT: E   22 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8047 (mm110)
REVERT: E   25 ARG cc_start: 0.7194 (tmm-80) cc_final: 0.6919 (tmm-80)
REVERT: E   28 ARG cc_start: 0.7263 (mmp80) cc_final: 0.6986 (mmm-85)
REVERT: E   53 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7884 (tpt)
REVERT: E  185 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7831 (mt-10)
REVERT: E  204 ARG cc_start: 0.8193 (mmm160) cc_final: 0.7963 (mmm160)
REVERT: E  206 GLU cc_start: 0.8497 (tp30) cc_final: 0.7838 (tp30)
REVERT: E  228 GLU cc_start: 0.7573 (tp30) cc_final: 0.6968 (tp30)
REVERT: E  250 ARG cc_start: 0.7963 (pmt-80) cc_final: 0.7667 (tmt-80)
REVERT: E  310 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7198 (mm)
REVERT: E  329 GLU cc_start: 0.8896 (pm20) cc_final: 0.8591 (pm20)
REVERT: A  275 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7914 (tp)
  outliers start: 31
  outliers final: 9
  residues processed: 204
  average time/residue: 0.6345
  time to fit residues: 136.9470
Evaluate side-chains
  184 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 170
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain C residue   14 LYS
Chi-restraints excluded: chain D residue  104 ARG
Chi-restraints excluded: chain E residue   41 THR
Chi-restraints excluded: chain E residue   53 MET
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain E residue  310 LEU
Chi-restraints excluded: chain A residue  133 SER
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  275 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 77 optimal weight:    6.9990
   chunk 32 optimal weight:    0.5980
   chunk 88 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0170
   chunk 18 optimal weight:    0.4980
   chunk 19 optimal weight:    0.8980
   chunk 74 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 86 optimal weight:    7.9990
   chunk 107 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.5218

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  36 ASN
** E  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 290 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.123998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.086959 restraints weight = 15782.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 3.51
r_work: 0.3114 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9020  Z= 0.130
  Angle     :  0.680  14.073  12225  Z= 0.332
  Chirality :  0.044   0.186   1407
  Planarity :  0.004   0.047   1535
  Dihedral  :  4.280  24.329   1216
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 21.57 %
    Favored  : 76.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.12 (0.26), residues: 1097
  helix:  1.27 (0.27), residues: 374
  sheet: -0.32 (0.32), residues: 261
  loop : -1.01 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D 177 
 TYR   0.020   0.001   TYR E 285 
 PHE   0.012   0.001   PHE E 286 
 TRP   0.028   0.001   TRP A 104 
 HIS   0.002   0.000   HIS A 142 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.13 ( 9018)
  covalent geometry    : angle       0.68014 /  0.33 (12221)
  SS BOND              : bond        0.00367 /  0.19 (    2)
  SS BOND              : angle       0.68914 /  0.36 (    4)
  hydrogen bonds       : bond        0.03192 /  2.19 (  396)
  hydrogen bonds       : angle       4.43228 /  3.15 ( 1131)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 186
  time to evaluate  : 0.364 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.9348 (tm-30) cc_final: 0.9011 (pp30)
REVERT: B   96 ARG cc_start: 0.9039 (ttm110) cc_final: 0.8715 (ttm110)
REVERT: B  130 GLU cc_start: 0.8598 (mp0) cc_final: 0.8367 (mp0)
REVERT: B  217 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7756 (pmt)
REVERT: C   22 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8620 (tm-30)
REVERT: D   59 GLU cc_start: 0.8462 (pp20) cc_final: 0.8232 (pp20)
REVERT: D   60 LYS cc_start: 0.9314 (mptt) cc_final: 0.8997 (mmtp)
REVERT: D   63 GLU cc_start: 0.8423 (tt0) cc_final: 0.8115 (tt0)
REVERT: D   82 LYS cc_start: 0.8786 (tppt) cc_final: 0.8491 (tppp)
REVERT: D  104 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7227 (pmm-80)
REVERT: D  106 GLU cc_start: 0.8441 (pp20) cc_final: 0.8183 (pp20)
REVERT: D  110 MET cc_start: 0.8845 (ttt) cc_final: 0.8463 (tpt)
REVERT: D  235 ARG cc_start: 0.8552 (mmp-170) cc_final: 0.8193 (mmp-170)
REVERT: E   22 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8056 (mm110)
REVERT: E   24 ARG cc_start: 0.6871 (mtm110) cc_final: 0.6639 (mtm110)
REVERT: E   25 ARG cc_start: 0.7206 (tmm-80) cc_final: 0.6912 (tmm-80)
REVERT: E   28 ARG cc_start: 0.7275 (mmp80) cc_final: 0.6976 (mmm-85)
REVERT: E   53 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7611 (tpt)
REVERT: E  204 ARG cc_start: 0.8236 (mmm160) cc_final: 0.7975 (mmm160)
REVERT: E  228 GLU cc_start: 0.7619 (tp30) cc_final: 0.7010 (tp30)
REVERT: E  306 MET cc_start: 0.9267 (mmm) cc_final: 0.9001 (mmm)
REVERT: E  311 ASN cc_start: 0.6497 (p0) cc_final: 0.5901 (p0)
REVERT: A   51 PHE cc_start: 0.8523 (t80) cc_final: 0.8302 (t80)
REVERT: A  285 LEU cc_start: 0.8995 (mm) cc_final: 0.8588 (mm)
  outliers start: 22
  outliers final: 9
  residues processed: 194
  average time/residue: 0.6047
  time to fit residues: 124.7381
Evaluate side-chains
  189 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 177
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain D residue  104 ARG
Chi-restraints excluded: chain E residue   41 THR
Chi-restraints excluded: chain E residue   53 MET
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  133 SER
Chi-restraints excluded: chain A residue  245 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 58 optimal weight:    7.9990
   chunk 61 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 93 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 96 optimal weight:    0.0040
   chunk 107 optimal weight:    0.4980
   overall best weight:    0.5592

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.124157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.087314 restraints weight = 15680.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 3.49
r_work: 0.3126 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9020  Z= 0.131
  Angle     :  0.674  14.048  12225  Z= 0.328
  Chirality :  0.044   0.229   1407
  Planarity :  0.004   0.047   1535
  Dihedral  :  4.219  23.706   1216
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 23.74 %
    Favored  : 74.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.14 (0.26), residues: 1097
  helix:  1.28 (0.27), residues: 374
  sheet: -0.42 (0.32), residues: 263
  loop : -0.99 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 177 
 TYR   0.016   0.001   TYR E 285 
 PHE   0.020   0.001   PHE A 311 
 TRP   0.030   0.001   TRP A 104 
 HIS   0.002   0.000   HIS B  54 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.13 ( 9018)
  covalent geometry    : angle       0.67355 /  0.33 (12221)
  SS BOND              : bond        0.00317 /  0.16 (    2)
  SS BOND              : angle       0.64479 /  0.33 (    4)
  hydrogen bonds       : bond        0.03086 /  2.12 (  396)
  hydrogen bonds       : angle       4.33467 /  3.08 ( 1131)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 175
  time to evaluate  : 0.349 
Fit side-chains
REVERT: B   96 ARG cc_start: 0.9043 (ttm110) cc_final: 0.8716 (ttm110)
REVERT: B  130 GLU cc_start: 0.8656 (mp0) cc_final: 0.8432 (mp0)
REVERT: B  217 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7757 (pmt)
REVERT: C   22 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8592 (tm-30)
REVERT: D   59 GLU cc_start: 0.8398 (pp20) cc_final: 0.8117 (pp20)
REVERT: D   60 LYS cc_start: 0.9337 (mptt) cc_final: 0.8916 (mmtp)
REVERT: D   63 GLU cc_start: 0.8457 (tt0) cc_final: 0.8149 (tt0)
REVERT: D   82 LYS cc_start: 0.8777 (tppt) cc_final: 0.8485 (tppp)
REVERT: D  106 GLU cc_start: 0.8447 (pp20) cc_final: 0.8224 (pp20)
REVERT: D  177 ARG cc_start: 0.8384 (mmm-85) cc_final: 0.7847 (mmm160)
REVERT: D  235 ARG cc_start: 0.8550 (mmp-170) cc_final: 0.8199 (mmp-170)
REVERT: E   18 MET cc_start: 0.8138 (mmm) cc_final: 0.7334 (tpt)
REVERT: E   22 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8001 (mm110)
REVERT: E   25 ARG cc_start: 0.7207 (tmm-80) cc_final: 0.6906 (tmm-80)
REVERT: E   28 ARG cc_start: 0.7277 (mmp80) cc_final: 0.6973 (mmm-85)
REVERT: E   53 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7701 (tpt)
REVERT: E  204 ARG cc_start: 0.8296 (mmm160) cc_final: 0.8059 (mmm160)
REVERT: E  228 GLU cc_start: 0.7702 (tp30) cc_final: 0.7076 (tp30)
REVERT: E  250 ARG cc_start: 0.7190 (tmt-80) cc_final: 0.6720 (tmt170)
REVERT: E  311 ASN cc_start: 0.5891 (p0) cc_final: 0.5203 (p0)
REVERT: A  285 LEU cc_start: 0.9014 (mm) cc_final: 0.8604 (mm)
  outliers start: 15
  outliers final: 9
  residues processed: 181
  average time/residue: 0.5765
  time to fit residues: 111.1541
Evaluate side-chains
  180 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 169
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain E residue   41 THR
Chi-restraints excluded: chain E residue   53 MET
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  133 SER
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  245 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 26 optimal weight:    0.4980
   chunk 16 optimal weight:    4.9990
   chunk 43 optimal weight:    0.1980
   chunk 95 optimal weight:    4.9990
   chunk 79 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 94 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  36 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 232 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.123046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.086055 restraints weight = 15844.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 3.50
r_work: 0.3107 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9020  Z= 0.168
  Angle     :  0.696  14.384  12225  Z= 0.340
  Chirality :  0.044   0.199   1407
  Planarity :  0.004   0.047   1535
  Dihedral  :  4.309  24.252   1216
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 23.32 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.11 (0.26), residues: 1097
  helix:  1.28 (0.27), residues: 374
  sheet: -0.35 (0.32), residues: 264
  loop : -0.98 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  19 
 TYR   0.016   0.001   TYR E 285 
 PHE   0.015   0.001   PHE A 311 
 TRP   0.031   0.002   TRP A 104 
 HIS   0.002   0.001   HIS B  54 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00394 /  0.17 ( 9018)
  covalent geometry    : angle       0.69608 /  0.34 (12221)
  SS BOND              : bond        0.00321 /  0.17 (    2)
  SS BOND              : angle       0.71498 /  0.35 (    4)
  hydrogen bonds       : bond        0.03231 /  2.21 (  396)
  hydrogen bonds       : angle       4.36134 /  3.11 ( 1131)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 173
  time to evaluate  : 0.409 
Fit side-chains
REVERT: B   96 ARG cc_start: 0.9038 (ttm110) cc_final: 0.8693 (ttm110)
REVERT: B  130 GLU cc_start: 0.8691 (mp0) cc_final: 0.8439 (mp0)
REVERT: B  217 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7598 (pmt)
REVERT: D   59 GLU cc_start: 0.8440 (pp20) cc_final: 0.8159 (pp20)
REVERT: D   60 LYS cc_start: 0.9339 (mptt) cc_final: 0.8895 (mmtp)
REVERT: D   63 GLU cc_start: 0.8372 (tt0) cc_final: 0.8033 (tt0)
REVERT: D   82 LYS cc_start: 0.8822 (tppt) cc_final: 0.8529 (tppp)
REVERT: D  106 GLU cc_start: 0.8535 (pp20) cc_final: 0.8253 (pp20)
REVERT: D  177 ARG cc_start: 0.8378 (mmm-85) cc_final: 0.8143 (mmm-85)
REVERT: D  235 ARG cc_start: 0.8574 (mmp-170) cc_final: 0.8218 (mmp-170)
REVERT: E   18 MET cc_start: 0.8094 (mmm) cc_final: 0.7324 (tpt)
REVERT: E   22 GLN cc_start: 0.8409 (mm-40) cc_final: 0.7816 (mm110)
REVERT: E   25 ARG cc_start: 0.7221 (tmm-80) cc_final: 0.6838 (tmm-80)
REVERT: E   28 ARG cc_start: 0.7305 (mmp80) cc_final: 0.7030 (mmm-85)
REVERT: E   53 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7752 (tpt)
REVERT: E  204 ARG cc_start: 0.8348 (mmm160) cc_final: 0.8148 (mmm160)
REVERT: E  228 GLU cc_start: 0.7673 (tp30) cc_final: 0.7021 (tp30)
REVERT: E  250 ARG cc_start: 0.7388 (tmt-80) cc_final: 0.6934 (tmt170)
REVERT: E  255 TYR cc_start: 0.8443 (m-80) cc_final: 0.7773 (m-80)
REVERT: E  309 ASP cc_start: 0.9190 (p0) cc_final: 0.8973 (p0)
REVERT: E  311 ASN cc_start: 0.5946 (p0) cc_final: 0.5282 (p0)
REVERT: A  285 LEU cc_start: 0.9038 (mm) cc_final: 0.8626 (mm)
  outliers start: 20
  outliers final: 9
  residues processed: 182
  average time/residue: 0.5870
  time to fit residues: 113.3099
Evaluate side-chains
  185 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 174
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain E residue   41 THR
Chi-restraints excluded: chain E residue   53 MET
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  133 SER
Chi-restraints excluded: chain A residue  143 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 37 optimal weight:    0.0170
   chunk 57 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 29 optimal weight:    0.2980
   chunk 4 optimal weight:    0.5980
   chunk 66 optimal weight:    3.9990
   chunk 107 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9980
   chunk 65 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   overall best weight:    0.5418

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  75 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.124071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.087124 restraints weight = 15582.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 3.50
r_work: 0.3119 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9020  Z= 0.134
  Angle     :  0.709  15.388  12225  Z= 0.343
  Chirality :  0.044   0.194   1407
  Planarity :  0.004   0.051   1535
  Dihedral  :  4.258  23.307   1216
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 23.94 %
    Favored  : 74.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.10 (0.26), residues: 1097
  helix:  1.30 (0.28), residues: 374
  sheet: -0.40 (0.33), residues: 252
  loop : -0.93 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  19 
 TYR   0.017   0.001   TYR E 285 
 PHE   0.014   0.001   PHE A 311 
 TRP   0.040   0.002   TRP A 104 
 HIS   0.002   0.000   HIS A 112 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.13 ( 9018)
  covalent geometry    : angle       0.70856 /  0.34 (12221)
  SS BOND              : bond        0.00312 /  0.16 (    2)
  SS BOND              : angle       0.55621 /  0.28 (    4)
  hydrogen bonds       : bond        0.03068 /  2.13 (  396)
  hydrogen bonds       : angle       4.26441 /  3.04 ( 1131)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 175
  time to evaluate  : 0.347 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.9371 (tm-30) cc_final: 0.9095 (pp30)
REVERT: B   96 ARG cc_start: 0.9054 (ttm110) cc_final: 0.8711 (ttm110)
REVERT: B  130 GLU cc_start: 0.8719 (mp0) cc_final: 0.8419 (mp0)
REVERT: D   60 LYS cc_start: 0.9330 (mptt) cc_final: 0.8977 (mmtp)
REVERT: D   63 GLU cc_start: 0.8382 (tt0) cc_final: 0.8076 (tt0)
REVERT: D   82 LYS cc_start: 0.8792 (tppt) cc_final: 0.8502 (tppp)
REVERT: D  106 GLU cc_start: 0.8532 (pp20) cc_final: 0.8327 (pp20)
REVERT: D  177 ARG cc_start: 0.8427 (mmm-85) cc_final: 0.7908 (mmm160)
REVERT: D  235 ARG cc_start: 0.8559 (mmp-170) cc_final: 0.8213 (mmp-170)
REVERT: E   18 MET cc_start: 0.8082 (mmm) cc_final: 0.7344 (tpt)
REVERT: E   22 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8063 (mm110)
REVERT: E   25 ARG cc_start: 0.7256 (tmm-80) cc_final: 0.6999 (tmm-80)
REVERT: E   28 ARG cc_start: 0.7312 (mmp80) cc_final: 0.7031 (mmm-85)
REVERT: E   53 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7777 (tpt)
REVERT: E  204 ARG cc_start: 0.8316 (mmm160) cc_final: 0.8031 (mmm160)
REVERT: E  228 GLU cc_start: 0.7638 (tp30) cc_final: 0.7116 (tp30)
REVERT: E  250 ARG cc_start: 0.7454 (tmt-80) cc_final: 0.7084 (tmt-80)
REVERT: E  255 TYR cc_start: 0.8348 (m-80) cc_final: 0.7746 (m-80)
REVERT: E  311 ASN cc_start: 0.6012 (p0) cc_final: 0.5631 (p0)
REVERT: A  195 THR cc_start: 0.6442 (OUTLIER) cc_final: 0.6205 (t)
REVERT: A  285 LEU cc_start: 0.8989 (mm) cc_final: 0.8587 (mm)
  outliers start: 19
  outliers final: 10
  residues processed: 185
  average time/residue: 0.6160
  time to fit residues: 120.9127
Evaluate side-chains
  181 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 169
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain E residue   41 THR
Chi-restraints excluded: chain E residue   53 MET
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  133 SER
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  245 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 81 optimal weight:    0.5980
   chunk 43 optimal weight:    0.0980
   chunk 101 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 52 optimal weight:    7.9990
   chunk 103 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 96 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  36 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.124810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.088403 restraints weight = 15653.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 3.48
r_work: 0.3131 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9020  Z= 0.139
  Angle     :  0.736  15.213  12225  Z= 0.356
  Chirality :  0.044   0.208   1407
  Planarity :  0.004   0.053   1535
  Dihedral  :  4.276  23.066   1216
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 25.18 %
    Favored  : 72.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.08 (0.26), residues: 1097
  helix:  1.34 (0.28), residues: 373
  sheet: -0.43 (0.33), residues: 252
  loop : -0.91 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  19 
 TYR   0.019   0.001   TYR E 285 
 PHE   0.011   0.001   PHE A 311 
 TRP   0.043   0.002   TRP A 104 
 HIS   0.002   0.000   HIS B  54 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.14 ( 9018)
  covalent geometry    : angle       0.73589 /  0.36 (12221)
  SS BOND              : bond        0.00284 /  0.15 (    2)
  SS BOND              : angle       0.62730 /  0.31 (    4)
  hydrogen bonds       : bond        0.03043 /  2.10 (  396)
  hydrogen bonds       : angle       4.21891 /  3.01 ( 1131)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 174
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 GLN cc_start: 0.9396 (tm-30) cc_final: 0.9161 (pp30)
REVERT: B   59 TYR cc_start: 0.7353 (m-80) cc_final: 0.7011 (m-80)
REVERT: B   96 ARG cc_start: 0.9106 (ttm110) cc_final: 0.8757 (ttm110)
REVERT: B  130 GLU cc_start: 0.8769 (mp0) cc_final: 0.8476 (mp0)
REVERT: D   63 GLU cc_start: 0.8392 (tt0) cc_final: 0.8091 (tt0)
REVERT: D   82 LYS cc_start: 0.8783 (tppt) cc_final: 0.8489 (tppp)
REVERT: D  106 GLU cc_start: 0.8497 (pp20) cc_final: 0.8292 (pp20)
REVERT: D  235 ARG cc_start: 0.8567 (mmp-170) cc_final: 0.8272 (mmp-170)
REVERT: E   18 MET cc_start: 0.8055 (mmm) cc_final: 0.7348 (tpp)
REVERT: E   22 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7807 (mm110)
REVERT: E   24 ARG cc_start: 0.6761 (mtm110) cc_final: 0.6555 (mtm110)
REVERT: E   25 ARG cc_start: 0.7235 (tmm-80) cc_final: 0.6867 (tmm-80)
REVERT: E   28 ARG cc_start: 0.7316 (mmp80) cc_final: 0.7050 (mmm-85)
REVERT: E   53 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7763 (tpt)
REVERT: E  204 ARG cc_start: 0.8322 (mmm160) cc_final: 0.8044 (mmm160)
REVERT: E  228 GLU cc_start: 0.7607 (tp30) cc_final: 0.7056 (tp30)
REVERT: E  250 ARG cc_start: 0.7493 (tmt-80) cc_final: 0.6988 (tmt170)
REVERT: E  255 TYR cc_start: 0.8319 (m-80) cc_final: 0.7700 (m-80)
REVERT: E  311 ASN cc_start: 0.5983 (p0) cc_final: 0.5392 (p0)
REVERT: A  195 THR cc_start: 0.6349 (OUTLIER) cc_final: 0.6126 (t)
REVERT: A  208 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7447 (t0)
REVERT: A  285 LEU cc_start: 0.8974 (mm) cc_final: 0.8552 (mm)
  outliers start: 19
  outliers final: 10
  residues processed: 186
  average time/residue: 0.5777
  time to fit residues: 114.1955
Evaluate side-chains
  178 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 165
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain E residue   41 THR
Chi-restraints excluded: chain E residue   53 MET
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  133 SER
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  208 ASP
Chi-restraints excluded: chain A residue  245 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0670
   chunk 88 optimal weight:    0.3980
   overall best weight:    0.8922

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 203 GLN
** E  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.123799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.087199 restraints weight = 15790.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 3.50
r_work: 0.3113 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9020  Z= 0.161
  Angle     :  0.762  15.198  12225  Z= 0.369
  Chirality :  0.045   0.210   1407
  Planarity :  0.004   0.054   1535
  Dihedral  :  4.379  22.401   1216
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 26.21 %
    Favored  : 72.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.05 (0.26), residues: 1097
  helix:  1.36 (0.28), residues: 373
  sheet: -0.40 (0.33), residues: 254
  loop : -0.91 (0.30), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  19 
 TYR   0.019   0.001   TYR E 285 
 PHE   0.011   0.001   PHE E 286 
 TRP   0.046   0.002   TRP A 104 
 HIS   0.002   0.001   HIS E 281 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00380 /  0.16 ( 9018)
  covalent geometry    : angle       0.76234 /  0.37 (12221)
  SS BOND              : bond        0.00297 /  0.16 (    2)
  SS BOND              : angle       0.78310 /  0.38 (    4)
  hydrogen bonds       : bond        0.03117 /  2.14 (  396)
  hydrogen bonds       : angle       4.29965 /  3.06 ( 1131)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 175
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 GLN cc_start: 0.9391 (tm-30) cc_final: 0.9159 (pp30)
REVERT: B   44 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8247 (mp10)
REVERT: B   59 TYR cc_start: 0.7217 (m-80) cc_final: 0.6865 (m-80)
REVERT: B   96 ARG cc_start: 0.9109 (ttm110) cc_final: 0.8867 (ttm110)
REVERT: B  130 GLU cc_start: 0.8793 (mp0) cc_final: 0.8496 (mp0)
REVERT: C   14 LYS cc_start: 0.9528 (ttpp) cc_final: 0.9151 (mppt)
REVERT: D   63 GLU cc_start: 0.8381 (tt0) cc_final: 0.8066 (tt0)
REVERT: D   82 LYS cc_start: 0.8813 (tppt) cc_final: 0.8525 (tppp)
REVERT: D  235 ARG cc_start: 0.8582 (mmp-170) cc_final: 0.8294 (mmp-170)
REVERT: E   18 MET cc_start: 0.8064 (mmm) cc_final: 0.7369 (tpp)
REVERT: E   22 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8067 (mm110)
REVERT: E   24 ARG cc_start: 0.6786 (mtm110) cc_final: 0.6567 (mtm110)
REVERT: E   25 ARG cc_start: 0.7236 (tmm-80) cc_final: 0.6964 (tmm-80)
REVERT: E   28 ARG cc_start: 0.7312 (mmp80) cc_final: 0.7049 (mmm-85)
REVERT: E   53 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7656 (tpt)
REVERT: E  204 ARG cc_start: 0.8325 (mmm160) cc_final: 0.8056 (mmm160)
REVERT: E  228 GLU cc_start: 0.7587 (tp30) cc_final: 0.7054 (tp30)
REVERT: E  250 ARG cc_start: 0.7543 (tmt-80) cc_final: 0.7155 (tmt170)
REVERT: E  255 TYR cc_start: 0.8319 (m-80) cc_final: 0.7720 (m-80)
REVERT: A  195 THR cc_start: 0.6357 (OUTLIER) cc_final: 0.6133 (t)
REVERT: A  208 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7505 (t0)
  outliers start: 15
  outliers final: 10
  residues processed: 183
  average time/residue: 0.6155
  time to fit residues: 119.3993
Evaluate side-chains
  175 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 162
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain E residue   41 THR
Chi-restraints excluded: chain E residue   53 MET
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  133 SER
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  208 ASP
Chi-restraints excluded: chain A residue  245 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 106 optimal weight:    0.9980
   chunk 95 optimal weight:    0.8980
   chunk 79 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0870
   chunk 61 optimal weight:    5.9990
   chunk 72 optimal weight:    0.6980
   chunk 100 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 109 optimal weight:    5.9990
   overall best weight:    0.6358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  36 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 203 GLN
E  52 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.124547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.087970 restraints weight = 15577.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 3.48
r_work: 0.3141 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9020  Z= 0.151
  Angle     :  0.798  19.558  12225  Z= 0.380
  Chirality :  0.045   0.207   1407
  Planarity :  0.004   0.056   1535
  Dihedral  :  4.416  21.672   1216
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 25.59 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.03 (0.26), residues: 1097
  helix:  1.35 (0.28), residues: 373
  sheet: -0.27 (0.33), residues: 245
  loop : -0.95 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  19 
 TYR   0.017   0.001   TYR A 165 
 PHE   0.020   0.001   PHE A 311 
 TRP   0.054   0.002   TRP A 104 
 HIS   0.002   0.000   HIS B 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.15 ( 9018)
  covalent geometry    : angle       0.79813 /  0.38 (12221)
  SS BOND              : bond        0.00302 /  0.16 (    2)
  SS BOND              : angle       0.77251 /  0.38 (    4)
  hydrogen bonds       : bond        0.03093 /  2.13 (  396)
  hydrogen bonds       : angle       4.31112 /  3.06 ( 1131)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3734.23 seconds
wall clock time: 64 minutes 23.97 seconds (3863.97 seconds total)