Starting phenix.real_space_refine
on Thu Mar 13 17:52:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xgo_38329/03_2025/8xgo_38329.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xgo_38329/03_2025/8xgo_38329.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xgo_38329/03_2025/8xgo_38329.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xgo_38329/03_2025/8xgo_38329.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xgo_38329/03_2025/8xgo_38329.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xgo_38329/03_2025/8xgo_38329.cif"
  }
  resolution = 2.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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      59      5.16       5
     C    5754      2.51       5
     N    1568      2.21       5
     O    1664      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9045
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2309
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2309
          Classifications: {'peptide': 299}
          Link IDs: {'PTRANS': 18, 'TRANS': 280}
    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: 1791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1791
          Classifications: {'peptide': 233}
          Link IDs: {'PTRANS': 10, 'TRANS': 222}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1880
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 5, 'TRANS': 222}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 31
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 3, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'UYA:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "F"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 56
          Unusual residues: {'XZA': 1}
          Classifications: {'peptide': 5, 'undetermined': 1}
          Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1}
          Link IDs: {'CIS': 1, 'TRANS': 2, None: 2}
            Not linked:
              pdbres="PHE F   6 "
              pdbres="XZA F   7 "
            Not linked:
              pdbres="XZA F   7 "
              pdbres="LEU F   8 "
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'NMM:plan-2': 1, 'XZA:plan-1': 1}
          Unresolved non-hydrogen planarities: 2
    Chain: "F"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.76, per 1000 atoms: 0.64
  Number of scatterers: 9045
  At special positions: 0
  Unit cell: (88.81, 122.84, 128.65, 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      59     16.00
     O    1664      8.00
     N    1568      7.00
     C    5754      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 115 " - pdb=" SG  CYS A 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  39 " - pdb=" SG  CYS D 113 " 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=3, symmetry=0
  Links applied
    TRANS
      " DTH F   5 " - " ASN F   4 "
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.98
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DTH F   5 "
      Input volumes are d-peptide like
        pdb=" CB  UYA F   3 "
        pdb=" CB  PHE F   6 "
  Number of C-beta restraints generated:  2160

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      37.2% alpha, 20.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 45
      removed outlier: 4.230A  pdb=" N   TRP A  43 " --> pdb=" O   ALA A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 70
      removed outlier: 3.746A  pdb=" N   PHE A  49 " --> pdb=" O   VAL A  45 " (cutoff:3.500A)
      removed outlier: 5.933A  pdb=" N   ALA A  51 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU A  62 " --> pdb=" O   VAL A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 74
    Processing helix  chain 'A' and resid 75 through 102
      Proline residue:  A  97  - end of helix
    Processing helix  chain 'A' and resid 111 through 146
      removed outlier: 3.620A  pdb=" N   LYS A 116 " --> pdb=" O   ASP A 112 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   GLN A 123 " --> pdb=" O   ASN A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 153
      removed outlier: 4.303A  pdb=" N   HIS A 152 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 175
    Processing helix  chain 'A' and resid 176 through 179
    Processing helix  chain 'A' and resid 197 through 213
    Processing helix  chain 'A' and resid 213 through 236
      removed outlier: 4.170A  pdb=" N   ALA A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 288
      removed outlier: 3.503A  pdb=" N   VAL A 249 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      Proline residue:  A 278  - end of helix
    Processing helix  chain 'A' and resid 298 through 324
      removed outlier: 3.755A  pdb=" N   SER A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
      Proline residue:  A 320  - end of helix
    Processing helix  chain 'A' and resid 327 through 336
    Processing helix  chain 'B' and resid 9 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 10 through 24
      removed outlier: 3.556A  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 'E' and resid 6 through 31
    Processing helix  chain 'E' and resid 45 through 57
    Processing helix  chain 'E' and resid 206 through 215
      removed outlier: 4.364A  pdb=" N   ILE E 211 " --> pdb=" O   ARG E 208 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   HIS E 212 " --> pdb=" O   LYS E 209 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 227 through 229
      No H-bonds generated for 'chain 'E' and resid 227 through 229'
    Processing helix  chain 'E' and resid 240 through 247
      removed outlier: 3.501A  pdb=" N   GLU E 244 " --> pdb=" O   ASN E 240 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 248 through 254
    Processing helix  chain 'E' and resid 269 through 277
    Processing helix  chain 'E' and resid 281 through 286
      removed outlier: 4.048A  pdb=" N   TYR E 285 " --> pdb=" O   HIS E 281 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 297 through 309
    Processing helix  chain 'E' and resid 329 through 350
    Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 184
      removed outlier: 3.806A  pdb=" N   TYR A 190 " --> pdb=" O   SER A 184 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.353A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.618A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.922A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.096A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.906A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.815A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.478A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.727A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.667A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.650A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 20 through 24
    Processing sheet with id=AB1, first strand: chain 'D' and resid 75 through 77
    Processing sheet with id=AB2, first strand: chain 'D' and resid 62 through 63
    Processing sheet with id=AB3, first strand: chain 'D' and resid 157 through 158
    Processing sheet with id=AB4, first strand: chain 'D' and resid 211 through 212
      removed outlier: 6.518A  pdb=" N   TRP D 193 " --> pdb=" O   LEU D 205 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   TYR D 207 " --> pdb=" O   LEU D 191 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   LEU D 191 " --> pdb=" O   TYR D 207 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   GLY D 242 " --> pdb=" O   LEU D 262 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 184 through 189
      removed outlier: 6.951A  pdb=" N   LEU E  36 " --> pdb=" O   VAL E 198 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   SER E 219 " --> pdb=" O   LYS E  35 " (cutoff:3.500A)

    447 hydrogen bonds defined for protein.
    1260 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: 2.69

  Time building geometry restraints manager: 3.07 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1451
        1.30 -     1.43: 2495
        1.43 -     1.56: 5192
        1.56 -     1.69: 17
        1.69 -     1.82: 87
  Bond restraints: 9242
  Sorted by residual:
  bond pdb=" C   NMM F   9 "
       pdb=" N   TRP F  10 "
    ideal  model  delta    sigma   weight residual
    1.329  1.508 -0.179 1.40e-02 5.10e+03 1.64e+02
  bond pdb=" C   UYA F   3 "
       pdb=" N   ASN F   4 "
    ideal  model  delta    sigma   weight residual
    1.329  1.492 -0.163 1.40e-02 5.10e+03 1.36e+02
  bond pdb=" C   LEU F   8 "
       pdb=" N   NMM F   9 "
    ideal  model  delta    sigma   weight residual
    1.329  1.476 -0.147 1.40e-02 5.10e+03 1.11e+02
  bond pdb=" C   DTH F   5 "
       pdb=" N   PHE F   6 "
    ideal  model  delta    sigma   weight residual
    1.329  1.473 -0.144 1.40e-02 5.10e+03 1.06e+02
  bond pdb=" CB  UYA F   3 "
       pdb=" CG  UYA F   3 "
    ideal  model  delta    sigma   weight residual
    1.518  1.343  0.175 2.00e-02 2.50e+03 7.67e+01
  ... (remaining 9237 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.07: 12431
        3.07 -     6.15: 94
        6.15 -     9.22: 7
        9.22 -    12.30: 1
       12.30 -    15.37: 1
  Bond angle restraints: 12534
  Sorted by residual:
  angle pdb=" CA  ASN F   4 "
        pdb=" CB  ASN F   4 "
        pdb=" CG  ASN F   4 "
      ideal   model   delta    sigma   weight residual
     112.60  120.96   -8.36 1.00e+00 1.00e+00 6.99e+01
  angle pdb=" C   LEU E 310 "
        pdb=" N   ASN E 311 "
        pdb=" CA  ASN E 311 "
      ideal   model   delta    sigma   weight residual
     121.80  137.17  -15.37 2.44e+00 1.68e-01 3.97e+01
  angle pdb=" CA  DTH F   5 "
        pdb=" C   DTH F   5 "
        pdb=" N   PHE F   6 "
      ideal   model   delta    sigma   weight residual
     116.20  126.56  -10.36 2.00e+00 2.50e-01 2.68e+01
  angle pdb=" O   DTH F   5 "
        pdb=" C   DTH F   5 "
        pdb=" N   PHE F   6 "
      ideal   model   delta    sigma   weight residual
     123.00  117.04    5.96 1.60e+00 3.91e-01 1.39e+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  128.11   -6.57 1.91e+00 2.74e-01 1.18e+01
  ... (remaining 12529 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.43: 4993
       17.43 -    34.85: 404
       34.85 -    52.28: 58
       52.28 -    69.70: 14
       69.70 -    87.13: 12
  Dihedral angle restraints: 5481
    sinusoidal: 2130
      harmonic: 3351
  Sorted by residual:
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.00   26.00     0      5.00e+00 4.00e-02 2.70e+01
  dihedral pdb=" CA  LEU E 310 "
           pdb=" C   LEU E 310 "
           pdb=" N   ASN E 311 "
           pdb=" CA  ASN E 311 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.59  -22.41     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" CA  LYS E 246 "
           pdb=" C   LYS E 246 "
           pdb=" N   ALA E 247 "
           pdb=" CA  ALA E 247 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.09   20.91     0      5.00e+00 4.00e-02 1.75e+01
  ... (remaining 5478 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.006: 1411
       1.006 -    2.012: 0
       2.012 -    3.018: 0
       3.018 -    4.025: 0
       4.025 -    5.031: 1
  Chirality restraints: 1412
  Sorted by residual:
  chirality pdb=" CA  PHE F   6 "
            pdb=" N   PHE F   6 "
            pdb=" C   PHE F   6 "
            pdb=" CB  PHE F   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.52    5.03 2.00e-01 2.50e+01 6.33e+02
  chirality pdb=" CA  UYA F   3 "
            pdb=" N   UYA F   3 "
            pdb=" C   UYA F   3 "
            pdb=" CB  UYA F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -3.23    0.74 2.00e-01 2.50e+01 1.38e+01
  chirality pdb=" CA  LEU F   8 "
            pdb=" N   LEU F   8 "
            pdb=" C   LEU F   8 "
            pdb=" CB  LEU F   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.91   -0.40 2.00e-01 2.50e+01 3.97e+00
  ... (remaining 1409 not shown)

  Planarity restraints: 1594
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E 248 "    0.019 2.00e-02 2.50e+03   3.74e-02 1.40e+01
        pdb=" C   LEU E 248 "   -0.065 2.00e-02 2.50e+03
        pdb=" O   LEU E 248 "    0.024 2.00e-02 2.50e+03
        pdb=" N   PHE E 249 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A  48 "    0.017 2.00e-02 2.50e+03   3.40e-02 1.16e+01
        pdb=" C   PHE A  48 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   PHE A  48 "    0.022 2.00e-02 2.50e+03
        pdb=" N   PHE A  49 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 167 "   -0.030 5.00e-02 4.00e+02   4.53e-02 3.28e+00
        pdb=" N   PRO D 168 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO D 168 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO D 168 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1591 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 245
        2.70 -     3.25: 9031
        3.25 -     3.80: 14728
        3.80 -     4.35: 19516
        4.35 -     4.90: 32622
  Nonbonded interactions: 76142
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP D  90 "
            pdb=" NZ  LYS D  93 "
     model   vdw
     2.144 3.120
  nonbonded pdb=" NH1 ARG B  22 "
            pdb=" OD2 ASP B 258 "
     model   vdw
     2.157 3.120
  nonbonded pdb=" O   LEU A  57 "
            pdb=" OG  SER A  61 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" OH  TYR D 192 "
            pdb=" OE2 GLU E   8 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" NE2 HIS B  54 "
            pdb=" OG  SER B  72 "
     model   vdw
     2.211 3.120
  ... (remaining 76137 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:             2.250
  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:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     24.270
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  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:11.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
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      :  0.007   0.179   9242  Z= 0.452
  Angle     :  0.678  15.370  12534  Z= 0.366
  Chirality :  0.143   5.031   1412
  Planarity :  0.004   0.045   1593
  Dihedral  : 13.277  87.130   3312
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.41 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.26), residues: 1133
  helix:  1.54 (0.27), residues: 396
  sheet: -0.45 (0.32), residues: 255
  loop : -1.12 (0.30), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 193 
 HIS   0.003   0.001   HIS B  62 
 PHE   0.010   0.001   PHE C  61 
 TYR   0.019   0.001   TYR A 313 
 ARG   0.003   0.000   ARG B 256 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 183
  time to evaluate  : 0.931 
Fit side-chains
REVERT: A  332 GLN cc_start: 0.8336 (pp30) cc_final: 0.7999 (pp30)
REVERT: D  240 ASP cc_start: 0.8411 (m-30) cc_final: 0.7945 (m-30)
REVERT: D  241 VAL cc_start: 0.9270 (t) cc_final: 0.8993 (p)
REVERT: E  231 GLN cc_start: 0.8834 (mm110) cc_final: 0.8470 (mm110)
REVERT: E  259 GLN cc_start: 0.8726 (mm110) cc_final: 0.8487 (mm110)
REVERT: E  315 ASP cc_start: 0.7959 (p0) cc_final: 0.7713 (p0)
REVERT: F    6 PHE cc_start: 0.8087 (m-80) cc_final: 0.7868 (m-80)
  outliers start: 2
  outliers final: 1
  residues processed: 184
  average time/residue: 1.3847
  time to fit residues: 269.5910
Evaluate side-chains
  146 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    4 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0770
   chunk 57 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 101 optimal weight:    0.0070
   overall best weight:    1.0160

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

Flipped N/Q/H residues before XYZ refinement:
** A  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 GLN
A 286 GLN
B  44 GLN
B  75 GLN
D  99 GLN
D 203 GLN
E  22 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.091379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.067122 restraints weight = 17011.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.2906 rms_B_bonded: 2.91
r_work: 0.2755 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.1226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9242  Z= 0.245
  Angle     :  0.652  11.005  12534  Z= 0.329
  Chirality :  0.045   0.412   1412
  Planarity :  0.005   0.046   1593
  Dihedral  :  5.463  61.560   1274
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 11.05 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.26), residues: 1133
  helix:  1.65 (0.27), residues: 400
  sheet: -0.52 (0.31), residues: 268
  loop : -1.10 (0.30), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  62 
 PHE   0.014   0.001   PHE F   6 
 TYR   0.031   0.001   TYR A 313 
 ARG   0.007   0.001   ARG B  22 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 161
  time to evaluate  : 0.956 
Fit side-chains
REVERT: B  217 MET cc_start: 0.7726 (ptm) cc_final: 0.7126 (pp-130)
REVERT: C   21 MET cc_start: 0.8716 (tmm) cc_final: 0.8173 (tmm)
REVERT: D   28 LEU cc_start: 0.9171 (tt) cc_final: 0.8893 (tm)
REVERT: D   99 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8459 (tp40)
REVERT: D  240 ASP cc_start: 0.8538 (m-30) cc_final: 0.8138 (m-30)
REVERT: E   43 GLU cc_start: 0.8498 (pt0) cc_final: 0.7809 (pp20)
REVERT: E  231 GLN cc_start: 0.8794 (mm110) cc_final: 0.8203 (mm110)
REVERT: E  259 GLN cc_start: 0.9107 (mm110) cc_final: 0.8875 (mm110)
REVERT: E  327 ASP cc_start: 0.8459 (t0) cc_final: 0.8154 (t0)
  outliers start: 20
  outliers final: 6
  residues processed: 164
  average time/residue: 1.3862
  time to fit residues: 241.3622
Evaluate side-chains
  150 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 143
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue   99 GLN
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain F residue    4 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    2.3188

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

Flipped N/Q/H residues before XYZ refinement:
** A  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 286 GLN
B  44 GLN
B 156 GLN
D  99 GLN
D 203 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.087994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.063776 restraints weight = 17340.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.2836 rms_B_bonded: 2.88
r_work: 0.2680 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043   9242  Z= 0.437
  Angle     :  0.689  10.221  12534  Z= 0.351
  Chirality :  0.047   0.366   1412
  Planarity :  0.005   0.042   1593
  Dihedral  :  5.814  70.068   1274
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 15.50 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.26), residues: 1133
  helix:  1.68 (0.27), residues: 392
  sheet: -0.58 (0.31), residues: 268
  loop : -1.20 (0.29), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  99 
 HIS   0.005   0.001   HIS B  62 
 PHE   0.014   0.002   PHE A  48 
 TYR   0.028   0.002   TYR A 103 
 ARG   0.006   0.001   ARG C  27 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 1.023 
Fit side-chains
REVERT: A   54 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8935 (mm)
REVERT: B   19 ARG cc_start: 0.8885 (ttp-110) cc_final: 0.8454 (ttp-110)
REVERT: B   32 GLN cc_start: 0.8482 (pm20) cc_final: 0.8188 (pm20)
REVERT: B   44 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8501 (mm-40)
REVERT: B  217 MET cc_start: 0.8068 (ptm) cc_final: 0.7636 (ppp)
REVERT: B  260 GLU cc_start: 0.8233 (tp30) cc_final: 0.7912 (tp30)
REVERT: C   21 MET cc_start: 0.8689 (tmm) cc_final: 0.8257 (tmm)
REVERT: C   36 ASP cc_start: 0.8703 (m-30) cc_final: 0.8472 (m-30)
REVERT: D   28 LEU cc_start: 0.9148 (tt) cc_final: 0.8859 (tm)
REVERT: D  240 ASP cc_start: 0.8524 (m-30) cc_final: 0.8165 (m-30)
REVERT: E   43 GLU cc_start: 0.8435 (pt0) cc_final: 0.7818 (pp20)
REVERT: E  231 GLN cc_start: 0.8763 (mm110) cc_final: 0.8148 (mm110)
  outliers start: 24
  outliers final: 11
  residues processed: 158
  average time/residue: 1.3406
  time to fit residues: 224.7767
Evaluate side-chains
  148 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain E residue  244 GLU
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  350 TYR
Chi-restraints excluded: chain F residue    2 TYR
Chi-restraints excluded: chain F residue    4 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 60 optimal weight:    0.5980
   chunk 109 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 94 optimal weight:    0.7980
   chunk 111 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 286 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.091311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.065932 restraints weight = 16750.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.2877 rms_B_bonded: 2.99
r_work: 0.2720 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.1671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9242  Z= 0.214
  Angle     :  0.626   9.765  12534  Z= 0.315
  Chirality :  0.043   0.326   1412
  Planarity :  0.004   0.039   1593
  Dihedral  :  5.551  69.648   1274
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.25 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.26), residues: 1133
  helix:  1.82 (0.27), residues: 391
  sheet: -0.57 (0.31), residues: 268
  loop : -1.17 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 181 
 PHE   0.021   0.001   PHE A  48 
 TYR   0.019   0.001   TYR A 103 
 ARG   0.007   0.000   ARG C  27 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 153
  time to evaluate  : 1.244 
Fit side-chains
REVERT: A   54 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8931 (mm)
REVERT: B   19 ARG cc_start: 0.8892 (ttp-110) cc_final: 0.8463 (ttp-110)
REVERT: B   44 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8400 (mm-40)
REVERT: B  217 MET cc_start: 0.8062 (ptm) cc_final: 0.7649 (ppp)
REVERT: B  260 GLU cc_start: 0.8122 (tp30) cc_final: 0.7901 (tp30)
REVERT: C   21 MET cc_start: 0.8675 (tmm) cc_final: 0.8192 (tmm)
REVERT: C   36 ASP cc_start: 0.8702 (m-30) cc_final: 0.8410 (m-30)
REVERT: C   47 GLU cc_start: 0.8546 (mp0) cc_final: 0.8336 (mp0)
REVERT: D   28 LEU cc_start: 0.9125 (tt) cc_final: 0.8836 (tm)
REVERT: D  240 ASP cc_start: 0.8538 (m-30) cc_final: 0.8307 (m-30)
REVERT: E   43 GLU cc_start: 0.8440 (pt0) cc_final: 0.7771 (pp20)
REVERT: E  231 GLN cc_start: 0.8737 (mm110) cc_final: 0.8057 (mm110)
REVERT: E  327 ASP cc_start: 0.8492 (t0) cc_final: 0.8180 (t0)
  outliers start: 26
  outliers final: 12
  residues processed: 163
  average time/residue: 1.3548
  time to fit residues: 234.6837
Evaluate side-chains
  156 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain C residue   62 PHE
Chi-restraints excluded: chain D residue  174 ILE
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  350 TYR
Chi-restraints excluded: chain F residue    2 TYR
Chi-restraints excluded: chain F residue    4 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 37 optimal weight:    0.0980
   chunk 45 optimal weight:    0.9980
   chunk 80 optimal weight:   20.0000
   chunk 99 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 101 optimal weight:    0.8980
   chunk 108 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 106 optimal weight:    0.5980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 286 GLN
A 315 ASN
D  99 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.091472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.067167 restraints weight = 17023.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.2906 rms_B_bonded: 2.90
r_work: 0.2755 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9242  Z= 0.197
  Angle     :  0.618   9.291  12534  Z= 0.311
  Chirality :  0.043   0.316   1412
  Planarity :  0.004   0.038   1593
  Dihedral  :  5.296  68.769   1274
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.18 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.26), residues: 1133
  helix:  1.89 (0.27), residues: 392
  sheet: -0.45 (0.32), residues: 266
  loop : -1.15 (0.29), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B  62 
 PHE   0.021   0.001   PHE A  48 
 TYR   0.016   0.001   TYR A 103 
 ARG   0.007   0.000   ARG C  27 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 155
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8950 (mm)
REVERT: B   19 ARG cc_start: 0.8915 (ttp-110) cc_final: 0.8687 (ttp-110)
REVERT: B   32 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8291 (pm20)
REVERT: B   44 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8350 (mm-40)
REVERT: B  217 MET cc_start: 0.8134 (ptm) cc_final: 0.7779 (ppp)
REVERT: C   21 MET cc_start: 0.8728 (tmm) cc_final: 0.8354 (tmm)
REVERT: C   36 ASP cc_start: 0.8743 (m-30) cc_final: 0.8474 (m-30)
REVERT: C   47 GLU cc_start: 0.8535 (mp0) cc_final: 0.8270 (mp0)
REVERT: D   36 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8913 (tppp)
REVERT: E   43 GLU cc_start: 0.8416 (pt0) cc_final: 0.7827 (pp20)
REVERT: E  231 GLN cc_start: 0.8759 (mm110) cc_final: 0.8107 (mm110)
REVERT: E  289 TYR cc_start: 0.8683 (t80) cc_final: 0.8343 (t80)
REVERT: E  327 ASP cc_start: 0.8497 (t0) cc_final: 0.8236 (t0)
  outliers start: 27
  outliers final: 15
  residues processed: 165
  average time/residue: 1.3377
  time to fit residues: 234.5765
Evaluate side-chains
  162 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   32 GLN
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain C residue   62 PHE
Chi-restraints excluded: chain D residue   36 LYS
Chi-restraints excluded: chain D residue  156 VAL
Chi-restraints excluded: chain D residue  174 ILE
Chi-restraints excluded: chain D residue  203 GLN
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  350 TYR
Chi-restraints excluded: chain F residue    2 TYR
Chi-restraints excluded: chain F residue    4 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 20 optimal weight:    9.9990
   chunk 59 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0970
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 286 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.090730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.066628 restraints weight = 16923.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.2892 rms_B_bonded: 2.87
r_work: 0.2741 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9242  Z= 0.255
  Angle     :  0.637   9.773  12534  Z= 0.321
  Chirality :  0.044   0.321   1412
  Planarity :  0.004   0.040   1593
  Dihedral  :  5.324  68.536   1274
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 18.90 %
    Favored  : 78.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.26), residues: 1133
  helix:  1.87 (0.27), residues: 392
  sheet: -0.49 (0.31), residues: 268
  loop : -1.11 (0.30), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B  62 
 PHE   0.022   0.001   PHE A  48 
 TYR   0.024   0.001   TYR A 103 
 ARG   0.007   0.000   ARG C  27 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 149
  time to evaluate  : 0.925 
Fit side-chains
REVERT: A   54 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8966 (mm)
REVERT: B   19 ARG cc_start: 0.8927 (ttp-110) cc_final: 0.8516 (ttp-110)
REVERT: B   32 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8246 (pm20)
REVERT: B   44 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8402 (mm-40)
REVERT: B  217 MET cc_start: 0.8174 (ptm) cc_final: 0.7810 (ppp)
REVERT: C   21 MET cc_start: 0.8765 (tmm) cc_final: 0.8388 (tmm)
REVERT: C   36 ASP cc_start: 0.8749 (m-30) cc_final: 0.8444 (m-30)
REVERT: C   42 GLU cc_start: 0.8432 (pp20) cc_final: 0.8225 (pt0)
REVERT: C   47 GLU cc_start: 0.8527 (mp0) cc_final: 0.8254 (mp0)
REVERT: D   28 LEU cc_start: 0.9095 (tt) cc_final: 0.8831 (tm)
REVERT: E   43 GLU cc_start: 0.8409 (pt0) cc_final: 0.7816 (pp20)
REVERT: E  231 GLN cc_start: 0.8742 (mm110) cc_final: 0.8117 (mm110)
REVERT: E  275 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8653 (mm-30)
REVERT: E  289 TYR cc_start: 0.8722 (t80) cc_final: 0.8352 (t80)
REVERT: E  327 ASP cc_start: 0.8499 (t0) cc_final: 0.8197 (t0)
  outliers start: 28
  outliers final: 16
  residues processed: 162
  average time/residue: 1.4518
  time to fit residues: 250.1554
Evaluate side-chains
  161 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 1.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  136 MET
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   32 GLN
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain C residue   62 PHE
Chi-restraints excluded: chain D residue  156 VAL
Chi-restraints excluded: chain D residue  174 ILE
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  350 TYR
Chi-restraints excluded: chain F residue    2 TYR
Chi-restraints excluded: chain F residue    4 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 286 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.090274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.066109 restraints weight = 17235.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.2882 rms_B_bonded: 2.89
r_work: 0.2730 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9242  Z= 0.264
  Angle     :  0.639   9.394  12534  Z= 0.323
  Chirality :  0.044   0.320   1412
  Planarity :  0.004   0.043   1593
  Dihedral  :  5.303  68.039   1274
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 19.42 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.26), residues: 1133
  helix:  1.89 (0.27), residues: 392
  sheet: -0.46 (0.32), residues: 268
  loop : -1.11 (0.30), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A  70 
 PHE   0.023   0.001   PHE A  48 
 TYR   0.022   0.001   TYR A 103 
 ARG   0.007   0.000   ARG C  27 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 151
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8974 (mm)
REVERT: B   19 ARG cc_start: 0.8930 (ttp-110) cc_final: 0.8512 (ttp-110)
REVERT: B   32 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8237 (pm20)
REVERT: B   44 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8405 (mm-40)
REVERT: B  217 MET cc_start: 0.8214 (ptm) cc_final: 0.7845 (ppp)
REVERT: C   21 MET cc_start: 0.8746 (tmm) cc_final: 0.8358 (tmm)
REVERT: C   36 ASP cc_start: 0.8750 (m-30) cc_final: 0.8428 (m-30)
REVERT: C   47 GLU cc_start: 0.8557 (mp0) cc_final: 0.8260 (mp0)
REVERT: D   28 LEU cc_start: 0.9078 (tt) cc_final: 0.8801 (tm)
REVERT: D  100 MET cc_start: 0.9322 (mtm) cc_final: 0.9070 (mtp)
REVERT: E   43 GLU cc_start: 0.8428 (pt0) cc_final: 0.7768 (pp20)
REVERT: E  204 ARG cc_start: 0.8410 (mmp80) cc_final: 0.7905 (mmp80)
REVERT: E  231 GLN cc_start: 0.8754 (mm110) cc_final: 0.8147 (mm110)
REVERT: E  275 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8659 (mm-30)
REVERT: E  289 TYR cc_start: 0.8723 (t80) cc_final: 0.8378 (t80)
REVERT: E  327 ASP cc_start: 0.8500 (t0) cc_final: 0.8191 (t0)
  outliers start: 27
  outliers final: 15
  residues processed: 163
  average time/residue: 1.6296
  time to fit residues: 281.4423
Evaluate side-chains
  159 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  136 MET
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   32 GLN
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain C residue   62 PHE
Chi-restraints excluded: chain D residue  108 THR
Chi-restraints excluded: chain D residue  156 VAL
Chi-restraints excluded: chain D residue  174 ILE
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  350 TYR
Chi-restraints excluded: chain F residue    2 TYR
Chi-restraints excluded: chain F residue    4 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 96 optimal weight:    0.6980
   chunk 30 optimal weight:    5.9990
   chunk 56 optimal weight:    0.8980
   chunk 108 optimal weight:    1.9990
   chunk 109 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   chunk 6 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 286 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.091318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.066986 restraints weight = 17204.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 2.91
r_work: 0.2751 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.1979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9242  Z= 0.210
  Angle     :  0.635   9.841  12534  Z= 0.319
  Chirality :  0.044   0.306   1412
  Planarity :  0.004   0.045   1593
  Dihedral  :  5.183  66.885   1274
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 20.35 %
    Favored  : 76.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.26), residues: 1133
  helix:  1.94 (0.27), residues: 391
  sheet: -0.59 (0.31), residues: 286
  loop : -1.10 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.002   0.001   HIS A  70 
 PHE   0.023   0.001   PHE A  48 
 TYR   0.020   0.001   TYR A 103 
 ARG   0.007   0.000   ARG C  27 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 150
  time to evaluate  : 1.031 
Fit side-chains
REVERT: A   54 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9001 (mm)
REVERT: B   19 ARG cc_start: 0.8927 (ttp-110) cc_final: 0.8526 (ttp-110)
REVERT: B   32 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8242 (pm20)
REVERT: B  217 MET cc_start: 0.8209 (ptm) cc_final: 0.7850 (ppp)
REVERT: B  234 PHE cc_start: 0.9473 (OUTLIER) cc_final: 0.8619 (m-80)
REVERT: B  259 GLN cc_start: 0.8391 (tt0) cc_final: 0.8093 (tt0)
REVERT: C   21 MET cc_start: 0.8727 (tmm) cc_final: 0.8324 (tmm)
REVERT: C   36 ASP cc_start: 0.8726 (m-30) cc_final: 0.8425 (m-30)
REVERT: C   47 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8215 (mp0)
REVERT: D   28 LEU cc_start: 0.9073 (tt) cc_final: 0.8800 (tm)
REVERT: D  100 MET cc_start: 0.9323 (mtm) cc_final: 0.9035 (mtp)
REVERT: E   43 GLU cc_start: 0.8417 (pt0) cc_final: 0.7798 (pp20)
REVERT: E  204 ARG cc_start: 0.8431 (mmp80) cc_final: 0.7896 (mmp80)
REVERT: E  231 GLN cc_start: 0.8733 (mm110) cc_final: 0.8156 (mm110)
REVERT: E  275 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8657 (mm-30)
REVERT: E  289 TYR cc_start: 0.8707 (t80) cc_final: 0.8364 (t80)
REVERT: E  327 ASP cc_start: 0.8458 (t0) cc_final: 0.8170 (t0)
  outliers start: 28
  outliers final: 18
  residues processed: 166
  average time/residue: 1.2936
  time to fit residues: 228.4054
Evaluate side-chains
  164 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  136 MET
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   32 GLN
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   62 PHE
Chi-restraints excluded: chain D residue  108 THR
Chi-restraints excluded: chain D residue  156 VAL
Chi-restraints excluded: chain D residue  174 ILE
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  350 TYR
Chi-restraints excluded: chain F residue    2 TYR
Chi-restraints excluded: chain F residue    4 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9980
   chunk 62 optimal weight:    8.9990
   chunk 15 optimal weight:    4.9990
   chunk 20 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 286 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  99 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 = 0.3311 r_free = 0.3311 target = 0.089276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.064921 restraints weight = 16992.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.2860 rms_B_bonded: 2.88
r_work: 0.2707 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9242  Z= 0.327
  Angle     :  0.679  10.279  12534  Z= 0.343
  Chirality :  0.045   0.327   1412
  Planarity :  0.004   0.046   1593
  Dihedral  :  5.382  66.691   1274
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 21.49 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.26), residues: 1133
  helix:  1.87 (0.27), residues: 392
  sheet: -0.57 (0.31), residues: 282
  loop : -1.02 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  99 
 HIS   0.004   0.001   HIS A  70 
 PHE   0.025   0.001   PHE A  48 
 TYR   0.021   0.001   TYR A 103 
 ARG   0.007   0.000   ARG C  27 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 147
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9015 (mm)
REVERT: B   32 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8227 (pm20)
REVERT: B  217 MET cc_start: 0.8285 (ptm) cc_final: 0.7994 (ppp)
REVERT: C   21 MET cc_start: 0.8734 (tmm) cc_final: 0.8364 (tmm)
REVERT: C   36 ASP cc_start: 0.8758 (m-30) cc_final: 0.8454 (m-30)
REVERT: C   47 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8294 (mp0)
REVERT: D   28 LEU cc_start: 0.9098 (tt) cc_final: 0.8830 (tm)
REVERT: D  100 MET cc_start: 0.9341 (mtm) cc_final: 0.9046 (mtp)
REVERT: E   43 GLU cc_start: 0.8405 (pt0) cc_final: 0.7754 (pp20)
REVERT: E  204 ARG cc_start: 0.8426 (mmp80) cc_final: 0.7913 (mmp80)
REVERT: E  215 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8189 (tp30)
REVERT: E  231 GLN cc_start: 0.8706 (mm110) cc_final: 0.8087 (mm110)
REVERT: E  275 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8687 (mm-30)
REVERT: E  289 TYR cc_start: 0.8750 (t80) cc_final: 0.8482 (t80)
REVERT: E  327 ASP cc_start: 0.8478 (t0) cc_final: 0.8215 (t0)
  outliers start: 26
  outliers final: 15
  residues processed: 163
  average time/residue: 1.8114
  time to fit residues: 313.5034
Evaluate side-chains
  159 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  136 MET
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   32 GLN
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   62 PHE
Chi-restraints excluded: chain D residue  108 THR
Chi-restraints excluded: chain D residue  174 ILE
Chi-restraints excluded: chain E residue  215 GLU
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  350 TYR
Chi-restraints excluded: chain F residue    2 TYR
Chi-restraints excluded: chain F residue    4 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 75 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 94 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0970
   chunk 31 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
** A  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 286 GLN
D  20 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.091501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.067449 restraints weight = 17149.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.2909 rms_B_bonded: 2.88
r_work: 0.2758 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9242  Z= 0.210
  Angle     :  0.662  10.900  12534  Z= 0.332
  Chirality :  0.044   0.308   1412
  Planarity :  0.004   0.046   1593
  Dihedral  :  5.195  65.197   1274
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 22.21 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.26), residues: 1133
  helix:  1.94 (0.27), residues: 392
  sheet: -0.51 (0.31), residues: 280
  loop : -1.12 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A  70 
 PHE   0.026   0.001   PHE A  48 
 TYR   0.031   0.001   TYR A 103 
 ARG   0.009   0.000   ARG B  19 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 1.021 
Fit side-chains
REVERT: A   54 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9006 (mm)
REVERT: B   19 ARG cc_start: 0.8913 (ttp80) cc_final: 0.8517 (ttp-110)
REVERT: B   32 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8191 (pm20)
REVERT: B  217 MET cc_start: 0.8280 (ptm) cc_final: 0.8018 (ppp)
REVERT: B  234 PHE cc_start: 0.9492 (OUTLIER) cc_final: 0.8827 (m-80)
REVERT: C   21 MET cc_start: 0.8710 (tmm) cc_final: 0.8345 (tmm)
REVERT: C   36 ASP cc_start: 0.8729 (m-30) cc_final: 0.8422 (m-30)
REVERT: C   47 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8227 (mp0)
REVERT: D   28 LEU cc_start: 0.9100 (tt) cc_final: 0.8834 (tm)
REVERT: D  100 MET cc_start: 0.9326 (mtm) cc_final: 0.9099 (mtp)
REVERT: D  235 ARG cc_start: 0.8201 (mmm160) cc_final: 0.7876 (tpm-80)
REVERT: E   43 GLU cc_start: 0.8417 (pt0) cc_final: 0.7813 (pp20)
REVERT: E  204 ARG cc_start: 0.8446 (mmp80) cc_final: 0.7938 (mmp80)
REVERT: E  215 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8188 (tp30)
REVERT: E  231 GLN cc_start: 0.8740 (mm110) cc_final: 0.8178 (mm110)
REVERT: E  275 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8703 (mm-30)
REVERT: E  289 TYR cc_start: 0.8702 (t80) cc_final: 0.8367 (t80)
REVERT: E  327 ASP cc_start: 0.8459 (t0) cc_final: 0.8221 (t0)
  outliers start: 23
  outliers final: 16
  residues processed: 159
  average time/residue: 1.3576
  time to fit residues: 229.3233
Evaluate side-chains
  163 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 142
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   32 GLN
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   62 PHE
Chi-restraints excluded: chain D residue   99 GLN
Chi-restraints excluded: chain D residue  108 THR
Chi-restraints excluded: chain D residue  174 ILE
Chi-restraints excluded: chain E residue  215 GLU
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  350 TYR
Chi-restraints excluded: chain F residue    2 TYR
Chi-restraints excluded: chain F residue    4 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 97 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 30 optimal weight:    6.9990
   chunk 72 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 286 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.091793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.067429 restraints weight = 17032.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.2910 rms_B_bonded: 2.91
r_work: 0.2760 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9242  Z= 0.217
  Angle     :  0.673  11.564  12534  Z= 0.337
  Chirality :  0.044   0.313   1412
  Planarity :  0.004   0.038   1593
  Dihedral  :  5.151  63.829   1274
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 22.11 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.26), residues: 1133
  helix:  1.94 (0.27), residues: 393
  sheet: -0.46 (0.32), residues: 278
  loop : -1.13 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A  70 
 PHE   0.027   0.001   PHE A  48 
 TYR   0.024   0.001   TYR A 103 
 ARG   0.007   0.000   ARG C  27 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6918.14 seconds
wall clock time: 122 minutes 50.24 seconds (7370.24 seconds total)