Starting phenix.real_space_refine
on Wed Sep 17 13:20:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xqs_38587/09_2025/8xqs_38587.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xqs_38587/09_2025/8xqs_38587.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xqs_38587/09_2025/8xqs_38587.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xqs_38587/09_2025/8xqs_38587.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xqs_38587/09_2025/8xqs_38587.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xqs_38587/09_2025/8xqs_38587.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
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: 5
    Type Number    sf(0)   Gaussians
     S      59      5.16       5
     C    5681      2.51       5
     N    1489      2.21       5
     O    1635      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8867
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1813
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1813
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2194
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2194
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 3, 'TRANS': 267}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 48
          Unusual residues: {'CLR': 1, 'FLF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.00, per 1000 atoms: 0.23
  Number of scatterers: 8867
  At special positions: 0
  Unit cell: (90.48, 118.56, 126.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      59     16.00
     F       3      9.00
     O    1635      8.00
     N    1489      7.00
     C    5681      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " 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: 0.84
  Conformation dependent library (CDL) restraints added in 377.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2102

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 13 sheets defined
      41.1% alpha, 22.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.779A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.665A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.544A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 3.744A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 4.662A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 8 through 24
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.140A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 62 through 65
      removed outlier: 3.551A  pdb=" N   LYS S  65 " --> pdb=" O   ASP S  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 62 through 65'
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.799A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 3 through 37
    Processing helix  chain 'R' and resid 42 through 72
      removed outlier: 3.757A  pdb=" N   PHE R  72 " --> pdb=" O   VAL R  68 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 73 through 77
    Processing helix  chain 'R' and resid 79 through 112
    Processing helix  chain 'R' and resid 116 through 124
      removed outlier: 4.240A  pdb=" N   TRP R 124 " --> pdb=" O   LEU R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 125 through 158
      removed outlier: 3.951A  pdb=" N   VAL R 139 " --> pdb=" O   LEU R 135 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   PHE R 140 " --> pdb=" O   VAL R 136 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   GLY R 158 " --> pdb=" O   ALA R 154 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 173 through 215
      removed outlier: 3.516A  pdb=" N   LEU R 181 " --> pdb=" O   SER R 177 " (cutoff:3.500A)
      Proline residue:  R 190  - end of helix
    Processing helix  chain 'R' and resid 231 through 252
      removed outlier: 4.099A  pdb=" N   ALA R 241 " --> pdb=" O   PHE R 237 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 257 through 284
      removed outlier: 4.088A  pdb=" N   ILE R 262 " --> pdb=" O   GLU R 258 " (cutoff:3.500A)
      removed outlier: 5.051A  pdb=" N   ILE R 263 " --> pdb=" O   GLU R 259 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   TYR R 272 " --> pdb=" O   MET R 268 " (cutoff:3.500A)
      Proline residue:  R 273  - end of helix
      removed outlier: 4.586A  pdb=" N   SER R 277 " --> pdb=" O   PRO R 273 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 284 through 299
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.977A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 8.076A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.306A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.640A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.220A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.895A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.712A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.643A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.569A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 6 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.892A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.763A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.980A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.988A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   GLY S 213 " --> pdb=" O   LEU S 233 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 143 through 148
      removed outlier: 3.645A  pdb=" N   PHE S 200 " --> pdb=" O   CYS S 147 " (cutoff:3.500A)

    487 hydrogen bonds defined for protein.
    1362 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: 1.35

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2818
        1.34 -     1.46: 2010
        1.46 -     1.58: 4138
        1.58 -     1.69: 0
        1.69 -     1.81: 87
  Bond restraints: 9053
  Sorted by residual:
  bond pdb=" N   FLF R 501 "
       pdb=" C1' FLF R 501 "
    ideal  model  delta    sigma   weight residual
    1.377  1.415 -0.038 2.00e-02 2.50e+03 3.67e+00
  bond pdb=" CB  PRO R  73 "
       pdb=" CG  PRO R  73 "
    ideal  model  delta    sigma   weight residual
    1.492  1.574 -0.082 5.00e-02 4.00e+02 2.72e+00
  bond pdb=" N   FLF R 501 "
       pdb=" C6  FLF R 501 "
    ideal  model  delta    sigma   weight residual
    1.378  1.409 -0.031 2.00e-02 2.50e+03 2.42e+00
  bond pdb=" CB  VAL A 339 "
       pdb=" CG1 VAL A 339 "
    ideal  model  delta    sigma   weight residual
    1.521  1.475  0.046 3.30e-02 9.18e+02 1.94e+00
  bond pdb=" C1  FLF R 501 "
       pdb=" C7  FLF R 501 "
    ideal  model  delta    sigma   weight residual
    1.521  1.495  0.026 2.00e-02 2.50e+03 1.66e+00
  ... (remaining 9048 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 12007
        1.77 -     3.54: 199
        3.54 -     5.31: 34
        5.31 -     7.07: 8
        7.07 -     8.84: 4
  Bond angle restraints: 12252
  Sorted by residual:
  angle pdb=" N   ALA B 203 "
        pdb=" CA  ALA B 203 "
        pdb=" C   ALA B 203 "
      ideal   model   delta    sigma   weight residual
     108.34  115.02   -6.68 1.31e+00 5.83e-01 2.60e+01
  angle pdb=" CA  TYR A 230 "
        pdb=" CB  TYR A 230 "
        pdb=" CG  TYR A 230 "
      ideal   model   delta    sigma   weight residual
     113.90  119.51   -5.61 1.80e+00 3.09e-01 9.72e+00
  angle pdb=" N   TYR S 223 "
        pdb=" CA  TYR S 223 "
        pdb=" C   TYR S 223 "
      ideal   model   delta    sigma   weight residual
     109.81  115.96   -6.15 2.21e+00 2.05e-01 7.75e+00
  angle pdb=" CA  ASP B 258 "
        pdb=" CB  ASP B 258 "
        pdb=" CG  ASP B 258 "
      ideal   model   delta    sigma   weight residual
     112.60  115.25   -2.65 1.00e+00 1.00e+00 7.00e+00
  angle pdb=" CA  LEU R  58 "
        pdb=" CB  LEU R  58 "
        pdb=" CG  LEU R  58 "
      ideal   model   delta    sigma   weight residual
     116.30  125.14   -8.84 3.50e+00 8.16e-02 6.38e+00
  ... (remaining 12247 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.74: 4543
       14.74 -    29.48: 596
       29.48 -    44.22: 203
       44.22 -    58.97: 46
       58.97 -    73.71: 3
  Dihedral angle restraints: 5391
    sinusoidal: 2143
      harmonic: 3248
  Sorted by residual:
  dihedral pdb=" CA  LYS A 210 "
           pdb=" C   LYS A 210 "
           pdb=" N   TRP A 211 "
           pdb=" CA  TRP A 211 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.07   19.93     0      5.00e+00 4.00e-02 1.59e+01
  dihedral pdb=" CA  TRP B  82 "
           pdb=" C   TRP B  82 "
           pdb=" N   ASP B  83 "
           pdb=" CA  ASP B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.31   18.69     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  GLU R  16 "
           pdb=" C   GLU R  16 "
           pdb=" N   PHE R  17 "
           pdb=" CA  PHE R  17 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.79   18.21     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 5388 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1214
       0.061 -    0.121: 167
       0.121 -    0.182: 16
       0.182 -    0.243: 1
       0.243 -    0.303: 1
  Chirality restraints: 1399
  Sorted by residual:
  chirality pdb=" CB  VAL A 201 "
            pdb=" CA  VAL A 201 "
            pdb=" CG1 VAL A 201 "
            pdb=" CG2 VAL A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.30e+00
  chirality pdb=" CG  LEU C  50 "
            pdb=" CB  LEU C  50 "
            pdb=" CD1 LEU C  50 "
            pdb=" CD2 LEU C  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.33e-01
  chirality pdb=" CA  PRO R  73 "
            pdb=" N   PRO R  73 "
            pdb=" C   PRO R  73 "
            pdb=" CB  PRO R  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.18 2.00e-01 2.50e+01 8.02e-01
  ... (remaining 1396 not shown)

  Planarity restraints: 1524
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C  59 "    0.070 5.00e-02 4.00e+02   1.06e-01 1.81e+01
        pdb=" N   PRO C  60 "   -0.184 5.00e-02 4.00e+02
        pdb=" CA  PRO C  60 "    0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO C  60 "    0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE R  72 "    0.052 5.00e-02 4.00e+02   7.68e-02 9.43e+00
        pdb=" N   PRO R  73 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO R  73 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO R  73 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 258 "   -0.011 2.00e-02 2.50e+03   2.25e-02 5.04e+00
        pdb=" C   ASP B 258 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ASP B 258 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLN B 259 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1521 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 151
        2.64 -     3.21: 8322
        3.21 -     3.77: 14449
        3.77 -     4.34: 19586
        4.34 -     4.90: 31664
  Nonbonded interactions: 74172
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.078 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 163 "
     model   vdw
     2.123 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" OE2 GLU A  14 "
            pdb=" OG  SER S  52 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   ILE R 249 "
            pdb=" OG1 THR R 253 "
     model   vdw
     2.231 3.040
  ... (remaining 74167 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:             1.200
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.750
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
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      :  0.004   0.082   9055  Z= 0.170
  Angle     :  0.599   8.842  12256  Z= 0.317
  Chirality :  0.043   0.303   1399
  Planarity :  0.005   0.106   1524
  Dihedral  : 15.226  73.708   3283
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 29.76 %
    Favored  : 69.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.26), residues: 1104
  helix:  1.90 (0.25), residues: 422
  sheet: -0.50 (0.31), residues: 278
  loop : -1.05 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 304 
 TYR   0.014   0.002   TYR A 230 
 PHE   0.026   0.002   PHE R 186 
 TRP   0.010   0.002   TRP B 297 
 HIS   0.008   0.001   HIS R 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 9053)
  covalent geometry    : angle       0.59894 (12252)
  SS BOND              : bond        0.00273 (    2)
  SS BOND              : angle       0.68560 (    4)
  hydrogen bonds       : bond        0.14340 (  480)
  hydrogen bonds       : angle       5.55966 ( 1362)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 272
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   47 GLU cc_start: 0.7361 (mp0) cc_final: 0.7101 (mp0)
REVERT: S  216 TYR cc_start: 0.8004 (m-80) cc_final: 0.7017 (m-80)
REVERT: R  212 MET cc_start: 0.7471 (mmm) cc_final: 0.7209 (mmm)
  outliers start: 3
  outliers final: 2
  residues processed: 273
  average time/residue: 0.1080
  time to fit residues: 39.1174
Evaluate side-chains
  281 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 279
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain S residue  162 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    0.0970
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    0.2980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.2980
   chunk 106 optimal weight:    0.4980
   overall best weight:    0.3578

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

Flipped N/Q/H residues before XYZ refinement:
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 260 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 = 0.3918 r_free = 0.3918 target = 0.147063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.128383 restraints weight = 14118.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 2.40
r_work: 0.3554 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.0984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9055  Z= 0.126
  Angle     :  0.531   8.189  12256  Z= 0.281
  Chirality :  0.041   0.170   1399
  Planarity :  0.004   0.069   1524
  Dihedral  :  5.436  52.711   1273
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 24.72 %
    Favored  : 71.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.26), residues: 1104
  helix:  2.07 (0.25), residues: 427
  sheet: -0.48 (0.30), residues: 289
  loop : -0.94 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 304 
 TYR   0.015   0.001   TYR S 178 
 PHE   0.013   0.001   PHE R  17 
 TRP   0.009   0.001   TRP B 297 
 HIS   0.005   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9053)
  covalent geometry    : angle       0.53064 (12252)
  SS BOND              : bond        0.00236 (    2)
  SS BOND              : angle       0.61280 (    4)
  hydrogen bonds       : bond        0.04118 (  480)
  hydrogen bonds       : angle       4.52522 ( 1362)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 274
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  215 PHE cc_start: 0.8514 (m-80) cc_final: 0.7817 (m-80)
REVERT: A  267 PHE cc_start: 0.8489 (m-10) cc_final: 0.8243 (m-10)
REVERT: A  350 ASP cc_start: 0.7858 (t0) cc_final: 0.7595 (t0)
REVERT: B   46 ARG cc_start: 0.7552 (mtm110) cc_final: 0.7332 (mtm-85)
REVERT: B   83 ASP cc_start: 0.7943 (t0) cc_final: 0.7503 (t0)
REVERT: B  187 VAL cc_start: 0.8064 (t) cc_final: 0.7721 (p)
REVERT: B  258 ASP cc_start: 0.7720 (t0) cc_final: 0.7475 (t0)
REVERT: C   47 GLU cc_start: 0.6997 (mp0) cc_final: 0.6706 (mp0)
REVERT: R   49 THR cc_start: 0.6841 (OUTLIER) cc_final: 0.6626 (p)
REVERT: R  212 MET cc_start: 0.7693 (mmm) cc_final: 0.7472 (mpp)
  outliers start: 41
  outliers final: 21
  residues processed: 289
  average time/residue: 0.1021
  time to fit residues: 40.0170
Evaluate side-chains
  286 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 264
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  226 THR
Chi-restraints excluded: chain S residue  231 THR
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue   60 TRP
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  141 LEU
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  182 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 80 optimal weight:    7.9990
   chunk 28 optimal weight:    0.0770
   chunk 42 optimal weight:    0.9990
   chunk 90 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.7340

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
B 239 ASN
B 259 GLN
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.145120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.126345 restraints weight = 14024.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 2.42
r_work: 0.3522 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.1189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9055  Z= 0.171
  Angle     :  0.553   9.350  12256  Z= 0.291
  Chirality :  0.041   0.180   1399
  Planarity :  0.004   0.058   1524
  Dihedral  :  5.291  52.765   1271
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 25.03 %
    Favored  : 70.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.25), residues: 1104
  helix:  2.03 (0.24), residues: 421
  sheet: -0.49 (0.30), residues: 287
  loop : -1.00 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG S  67 
 TYR   0.018   0.002   TYR S 178 
 PHE   0.014   0.001   PHE S 227 
 TRP   0.017   0.001   TRP A 211 
 HIS   0.005   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 9053)
  covalent geometry    : angle       0.55265 (12252)
  SS BOND              : bond        0.00289 (    2)
  SS BOND              : angle       0.71394 (    4)
  hydrogen bonds       : bond        0.04347 (  480)
  hydrogen bonds       : angle       4.46838 ( 1362)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 267
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 TRP cc_start: 0.8045 (p-90) cc_final: 0.7726 (p-90)
REVERT: A  215 PHE cc_start: 0.8652 (m-80) cc_final: 0.7940 (m-80)
REVERT: A  267 PHE cc_start: 0.8572 (m-10) cc_final: 0.8105 (m-10)
REVERT: A  350 ASP cc_start: 0.7885 (t0) cc_final: 0.7552 (t0)
REVERT: B   83 ASP cc_start: 0.8045 (t0) cc_final: 0.7794 (t70)
REVERT: B  269 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7531 (mm)
REVERT: C   47 GLU cc_start: 0.7057 (mp0) cc_final: 0.6737 (mp0)
REVERT: S   59 TYR cc_start: 0.7219 (m-10) cc_final: 0.6904 (m-10)
REVERT: S  135 VAL cc_start: 0.8460 (p) cc_final: 0.7976 (m)
REVERT: S  192 SER cc_start: 0.7855 (OUTLIER) cc_final: 0.7619 (p)
REVERT: R   16 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6932 (tm-30)
REVERT: R  212 MET cc_start: 0.7676 (mmm) cc_final: 0.7417 (mpp)
  outliers start: 42
  outliers final: 30
  residues processed: 285
  average time/residue: 0.0953
  time to fit residues: 37.0561
Evaluate side-chains
  299 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 267
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  162 LEU
Chi-restraints excluded: chain S residue  174 GLN
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  226 THR
Chi-restraints excluded: chain S residue  231 THR
Chi-restraints excluded: chain R residue   48 LEU
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  110 LYS
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  182 THR
Chi-restraints excluded: chain R residue  187 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 100 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   chunk 90 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0970
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B 266 HIS
R  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.145026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.126194 restraints weight = 14187.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 2.43
r_work: 0.3498 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.1394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9055  Z= 0.170
  Angle     :  0.543   8.913  12256  Z= 0.288
  Chirality :  0.041   0.181   1399
  Planarity :  0.004   0.050   1524
  Dihedral  :  5.264  53.977   1271
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 24.20 %
    Favored  : 70.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.25), residues: 1104
  helix:  2.02 (0.24), residues: 421
  sheet: -0.52 (0.30), residues: 289
  loop : -1.03 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R  55 
 TYR   0.018   0.002   TYR S 178 
 PHE   0.012   0.001   PHE S 227 
 TRP   0.013   0.001   TRP A 211 
 HIS   0.005   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 9053)
  covalent geometry    : angle       0.54306 (12252)
  SS BOND              : bond        0.00303 (    2)
  SS BOND              : angle       0.72496 (    4)
  hydrogen bonds       : bond        0.04256 (  480)
  hydrogen bonds       : angle       4.43799 ( 1362)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 266
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 PHE cc_start: 0.8586 (m-80) cc_final: 0.7959 (m-80)
REVERT: A  216 GLU cc_start: 0.7336 (tt0) cc_final: 0.7073 (tm-30)
REVERT: A  267 PHE cc_start: 0.8609 (m-10) cc_final: 0.8151 (m-10)
REVERT: A  350 ASP cc_start: 0.7876 (t0) cc_final: 0.7500 (t0)
REVERT: B   70 LEU cc_start: 0.8506 (tp) cc_final: 0.8228 (tt)
REVERT: B   83 ASP cc_start: 0.8068 (t0) cc_final: 0.7808 (t70)
REVERT: B  134 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.8123 (mtm-85)
REVERT: B  269 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7534 (mm)
REVERT: C   47 GLU cc_start: 0.7051 (mp0) cc_final: 0.6749 (mp0)
REVERT: S   59 TYR cc_start: 0.7187 (m-10) cc_final: 0.6866 (m-10)
REVERT: S  117 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6585 (tt)
REVERT: S  135 VAL cc_start: 0.8454 (p) cc_final: 0.7962 (m)
REVERT: S  174 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7702 (pt0)
REVERT: S  192 SER cc_start: 0.7828 (OUTLIER) cc_final: 0.7589 (p)
REVERT: R   16 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6598 (tm-30)
REVERT: R  212 MET cc_start: 0.7650 (mmm) cc_final: 0.7359 (mpp)
REVERT: R  270 MET cc_start: 0.5172 (ptm) cc_final: 0.4864 (ptm)
  outliers start: 50
  outliers final: 35
  residues processed: 291
  average time/residue: 0.0950
  time to fit residues: 37.7741
Evaluate side-chains
  300 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 261
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  117 LEU
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  162 LEU
Chi-restraints excluded: chain S residue  174 GLN
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  222 GLU
Chi-restraints excluded: chain S residue  226 THR
Chi-restraints excluded: chain S residue  231 THR
Chi-restraints excluded: chain R residue   44 VAL
Chi-restraints excluded: chain R residue   48 LEU
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue  110 LYS
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  182 THR
Chi-restraints excluded: chain R residue  187 ILE
Chi-restraints excluded: chain R residue  253 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 101 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   chunk 107 optimal weight:    0.7980
   chunk 82 optimal weight:    0.6980
   chunk 90 optimal weight:    5.9990
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.144411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.125811 restraints weight = 14208.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 2.39
r_work: 0.3488 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.1487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9055  Z= 0.180
  Angle     :  0.555   8.322  12256  Z= 0.293
  Chirality :  0.042   0.185   1399
  Planarity :  0.004   0.049   1524
  Dihedral  :  5.332  54.996   1271
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 24.20 %
    Favored  : 70.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.25), residues: 1104
  helix:  1.98 (0.24), residues: 421
  sheet: -0.51 (0.31), residues: 289
  loop : -1.02 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R  55 
 TYR   0.018   0.002   TYR S 178 
 PHE   0.019   0.002   PHE B 222 
 TRP   0.010   0.001   TRP R  98 
 HIS   0.005   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 9053)
  covalent geometry    : angle       0.55461 (12252)
  SS BOND              : bond        0.00313 (    2)
  SS BOND              : angle       0.71264 (    4)
  hydrogen bonds       : bond        0.04316 (  480)
  hydrogen bonds       : angle       4.49645 ( 1362)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 266
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 PHE cc_start: 0.8586 (m-80) cc_final: 0.7963 (m-80)
REVERT: A  216 GLU cc_start: 0.7312 (tt0) cc_final: 0.7066 (tm-30)
REVERT: A  267 PHE cc_start: 0.8626 (m-10) cc_final: 0.8271 (m-10)
REVERT: A  335 VAL cc_start: 0.8430 (t) cc_final: 0.7991 (p)
REVERT: A  350 ASP cc_start: 0.7882 (t0) cc_final: 0.7537 (t0)
REVERT: B   83 ASP cc_start: 0.8092 (t0) cc_final: 0.7813 (t70)
REVERT: B  134 ARG cc_start: 0.8369 (mtm-85) cc_final: 0.8108 (mtm-85)
REVERT: B  269 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7552 (mm)
REVERT: C   47 GLU cc_start: 0.6947 (mp0) cc_final: 0.6658 (mp0)
REVERT: S   59 TYR cc_start: 0.7152 (m-10) cc_final: 0.6922 (m-10)
REVERT: S  135 VAL cc_start: 0.8449 (p) cc_final: 0.8151 (t)
REVERT: S  192 SER cc_start: 0.7822 (OUTLIER) cc_final: 0.7601 (p)
REVERT: R   16 GLU cc_start: 0.6984 (tm-30) cc_final: 0.6226 (tm-30)
REVERT: R  123 LYS cc_start: 0.6619 (OUTLIER) cc_final: 0.6075 (mmmt)
REVERT: R  212 MET cc_start: 0.7671 (mmm) cc_final: 0.7444 (mmp)
REVERT: R  270 MET cc_start: 0.5225 (ptm) cc_final: 0.4739 (ptm)
  outliers start: 49
  outliers final: 35
  residues processed: 294
  average time/residue: 0.0971
  time to fit residues: 39.2324
Evaluate side-chains
  301 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 263
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  162 LEU
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  222 GLU
Chi-restraints excluded: chain S residue  226 THR
Chi-restraints excluded: chain S residue  231 THR
Chi-restraints excluded: chain S residue  235 LEU
Chi-restraints excluded: chain R residue   44 VAL
Chi-restraints excluded: chain R residue   48 LEU
Chi-restraints excluded: chain R residue   60 TRP
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue  110 LYS
Chi-restraints excluded: chain R residue  123 LYS
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  253 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0370
   chunk 107 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 27 optimal weight:    0.2980
   chunk 2 optimal weight:    0.7980
   chunk 94 optimal weight:    0.4980
   chunk 90 optimal weight:    5.9990
   chunk 35 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0060
   overall best weight:    0.2874

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
B  75 GLN
B  91 HIS
B 237 ASN
B 239 ASN
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.147307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.128765 restraints weight = 14159.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 2.40
r_work: 0.3562 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9055  Z= 0.116
  Angle     :  0.520   7.518  12256  Z= 0.273
  Chirality :  0.041   0.211   1399
  Planarity :  0.004   0.047   1524
  Dihedral  :  5.020  55.927   1271
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 24.72 %
    Favored  : 70.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.26), residues: 1104
  helix:  2.24 (0.24), residues: 416
  sheet: -0.25 (0.32), residues: 269
  loop : -0.95 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R  55 
 TYR   0.014   0.001   TYR S 178 
 PHE   0.015   0.001   PHE S 227 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 9053)
  covalent geometry    : angle       0.52022 (12252)
  SS BOND              : bond        0.00272 (    2)
  SS BOND              : angle       0.55825 (    4)
  hydrogen bonds       : bond        0.03837 (  480)
  hydrogen bonds       : angle       4.31980 ( 1362)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 266
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 PHE cc_start: 0.8665 (m-80) cc_final: 0.8020 (m-80)
REVERT: A  216 GLU cc_start: 0.7272 (tt0) cc_final: 0.6992 (tm-30)
REVERT: A  243 MET cc_start: 0.7569 (tpp) cc_final: 0.7272 (ttt)
REVERT: A  267 PHE cc_start: 0.8557 (m-10) cc_final: 0.8208 (m-10)
REVERT: A  298 GLU cc_start: 0.6478 (tp30) cc_final: 0.6232 (tp30)
REVERT: A  341 ASP cc_start: 0.7999 (t0) cc_final: 0.7710 (t0)
REVERT: A  350 ASP cc_start: 0.7861 (t0) cc_final: 0.7515 (t0)
REVERT: B   49 ARG cc_start: 0.7822 (mpt180) cc_final: 0.7002 (mpt180)
REVERT: B   70 LEU cc_start: 0.8509 (tp) cc_final: 0.8241 (tt)
REVERT: B   83 ASP cc_start: 0.7934 (t0) cc_final: 0.7716 (t0)
REVERT: B  134 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.8086 (mtm-85)
REVERT: B  259 GLN cc_start: 0.8800 (pt0) cc_final: 0.8582 (pt0)
REVERT: B  298 ASP cc_start: 0.8084 (m-30) cc_final: 0.7769 (m-30)
REVERT: C   21 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6473 (mpp)
REVERT: C   47 GLU cc_start: 0.6720 (mp0) cc_final: 0.6352 (mp0)
REVERT: S   59 TYR cc_start: 0.7046 (m-10) cc_final: 0.6820 (m-10)
REVERT: S   84 THR cc_start: 0.8170 (p) cc_final: 0.7853 (t)
REVERT: S  221 LEU cc_start: 0.8399 (mt) cc_final: 0.8141 (mt)
REVERT: R   16 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6206 (tm-30)
REVERT: R   58 LEU cc_start: 0.7794 (tp) cc_final: 0.7523 (tt)
REVERT: R  212 MET cc_start: 0.7658 (mmm) cc_final: 0.7372 (mpp)
REVERT: R  261 LEU cc_start: 0.7854 (mt) cc_final: 0.7511 (pp)
REVERT: R  270 MET cc_start: 0.5069 (ptm) cc_final: 0.4624 (ptm)
  outliers start: 48
  outliers final: 36
  residues processed: 291
  average time/residue: 0.0958
  time to fit residues: 38.7886
Evaluate side-chains
  290 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 253
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  222 GLU
Chi-restraints excluded: chain S residue  231 THR
Chi-restraints excluded: chain S residue  235 LEU
Chi-restraints excluded: chain R residue   44 VAL
Chi-restraints excluded: chain R residue   48 LEU
Chi-restraints excluded: chain R residue   60 TRP
Chi-restraints excluded: chain R residue   82 PHE
Chi-restraints excluded: chain R residue  110 LYS
Chi-restraints excluded: chain R residue  124 TRP
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  182 THR
Chi-restraints excluded: chain R residue  253 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 41 optimal weight:    0.4980
   chunk 93 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0870
   chunk 73 optimal weight:    4.9990
   chunk 76 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 64 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
A 241 ASN
B  16 ASN
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  24 ASN
** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.146322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.127616 restraints weight = 14060.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 2.39
r_work: 0.3514 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9055  Z= 0.144
  Angle     :  0.552   9.021  12256  Z= 0.287
  Chirality :  0.041   0.179   1399
  Planarity :  0.004   0.048   1524
  Dihedral  :  5.093  55.914   1271
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 26.67 %
    Favored  : 69.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.26), residues: 1104
  helix:  2.24 (0.24), residues: 416
  sheet: -0.37 (0.31), residues: 284
  loop : -0.87 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R  55 
 TYR   0.014   0.001   TYR S 178 
 PHE   0.021   0.001   PHE R  17 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 9053)
  covalent geometry    : angle       0.55209 (12252)
  SS BOND              : bond        0.00249 (    2)
  SS BOND              : angle       0.61283 (    4)
  hydrogen bonds       : bond        0.03982 (  480)
  hydrogen bonds       : angle       4.36091 ( 1362)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 258
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 PHE cc_start: 0.8598 (m-80) cc_final: 0.7969 (m-80)
REVERT: A  216 GLU cc_start: 0.7324 (tt0) cc_final: 0.7049 (tm-30)
REVERT: A  267 PHE cc_start: 0.8529 (m-10) cc_final: 0.8196 (m-10)
REVERT: A  341 ASP cc_start: 0.7995 (t0) cc_final: 0.7725 (t0)
REVERT: A  350 ASP cc_start: 0.7827 (t0) cc_final: 0.7488 (t0)
REVERT: B   70 LEU cc_start: 0.8531 (tp) cc_final: 0.8244 (tt)
REVERT: B  134 ARG cc_start: 0.8390 (mtm-85) cc_final: 0.8108 (mtm-85)
REVERT: B  232 ILE cc_start: 0.8459 (tp) cc_final: 0.8073 (tt)
REVERT: C   21 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6523 (mpp)
REVERT: C   47 GLU cc_start: 0.6770 (mp0) cc_final: 0.6439 (mp0)
REVERT: S   59 TYR cc_start: 0.7040 (m-10) cc_final: 0.6829 (m-10)
REVERT: S   84 THR cc_start: 0.8179 (p) cc_final: 0.7887 (t)
REVERT: S  135 VAL cc_start: 0.8404 (p) cc_final: 0.7902 (m)
REVERT: S  221 LEU cc_start: 0.8269 (mt) cc_final: 0.8000 (mt)
REVERT: R   16 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6134 (tm-30)
REVERT: R   58 LEU cc_start: 0.7650 (tp) cc_final: 0.7364 (tt)
REVERT: R  212 MET cc_start: 0.7673 (mmm) cc_final: 0.7377 (mmp)
REVERT: R  270 MET cc_start: 0.5102 (ptm) cc_final: 0.4651 (ptm)
  outliers start: 41
  outliers final: 33
  residues processed: 280
  average time/residue: 0.1015
  time to fit residues: 38.7375
Evaluate side-chains
  287 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 253
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  222 GLU
Chi-restraints excluded: chain S residue  231 THR
Chi-restraints excluded: chain S residue  235 LEU
Chi-restraints excluded: chain R residue   44 VAL
Chi-restraints excluded: chain R residue   48 LEU
Chi-restraints excluded: chain R residue   60 TRP
Chi-restraints excluded: chain R residue  110 LYS
Chi-restraints excluded: chain R residue  182 THR
Chi-restraints excluded: chain R residue  188 PHE
Chi-restraints excluded: chain R residue  253 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 72 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   chunk 21 optimal weight:    0.4980
   chunk 56 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0870
   chunk 82 optimal weight:    0.0470
   chunk 37 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.3656

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

Flipped N/Q/H residues before XYZ refinement:
A 241 ASN
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 260 ASN ** 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 = 0.3920 r_free = 0.3920 target = 0.147512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.128344 restraints weight = 14043.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 2.55
r_work: 0.3517 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7215
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9055  Z= 0.127
  Angle     :  0.547   7.400  12256  Z= 0.287
  Chirality :  0.041   0.168   1399
  Planarity :  0.004   0.047   1524
  Dihedral  :  4.996  56.354   1271
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 26.98 %
    Favored  : 68.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.26), residues: 1104
  helix:  2.29 (0.24), residues: 416
  sheet: -0.36 (0.31), residues: 286
  loop : -0.85 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R  55 
 TYR   0.013   0.001   TYR S 178 
 PHE   0.025   0.001   PHE B 222 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9053)
  covalent geometry    : angle       0.54650 (12252)
  SS BOND              : bond        0.00327 (    2)
  SS BOND              : angle       0.74546 (    4)
  hydrogen bonds       : bond        0.03812 (  480)
  hydrogen bonds       : angle       4.31615 ( 1362)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 250
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  215 PHE cc_start: 0.8609 (m-80) cc_final: 0.7982 (m-80)
REVERT: A  216 GLU cc_start: 0.7388 (tt0) cc_final: 0.7074 (tm-30)
REVERT: A  267 PHE cc_start: 0.8496 (m-10) cc_final: 0.8169 (m-10)
REVERT: A  341 ASP cc_start: 0.7983 (t0) cc_final: 0.7698 (t0)
REVERT: A  350 ASP cc_start: 0.7891 (t0) cc_final: 0.7516 (t0)
REVERT: B   49 ARG cc_start: 0.7805 (mpt180) cc_final: 0.6891 (mpt180)
REVERT: B   70 LEU cc_start: 0.8515 (tp) cc_final: 0.8225 (tt)
REVERT: B  118 ASP cc_start: 0.7914 (p0) cc_final: 0.7644 (p0)
REVERT: B  188 MET cc_start: 0.7683 (tpp) cc_final: 0.6391 (tpp)
REVERT: B  259 GLN cc_start: 0.8778 (pt0) cc_final: 0.8566 (pt0)
REVERT: B  336 LEU cc_start: 0.8085 (mt) cc_final: 0.7841 (mt)
REVERT: C   21 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6469 (mpp)
REVERT: C   47 GLU cc_start: 0.6755 (mp0) cc_final: 0.6464 (mp0)
REVERT: S   59 TYR cc_start: 0.7042 (m-10) cc_final: 0.6784 (m-10)
REVERT: S   84 THR cc_start: 0.8157 (p) cc_final: 0.7872 (t)
REVERT: S  221 LEU cc_start: 0.8202 (mt) cc_final: 0.7951 (mt)
REVERT: R   16 GLU cc_start: 0.6959 (tm-30) cc_final: 0.6221 (tm-30)
REVERT: R  212 MET cc_start: 0.7625 (mmm) cc_final: 0.7340 (mmp)
REVERT: R  270 MET cc_start: 0.5177 (ptm) cc_final: 0.4715 (ptm)
  outliers start: 43
  outliers final: 36
  residues processed: 273
  average time/residue: 0.0955
  time to fit residues: 35.9671
Evaluate side-chains
  284 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 247
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  222 GLU
Chi-restraints excluded: chain S residue  231 THR
Chi-restraints excluded: chain S residue  235 LEU
Chi-restraints excluded: chain R residue   44 VAL
Chi-restraints excluded: chain R residue   48 LEU
Chi-restraints excluded: chain R residue   60 TRP
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue  110 LYS
Chi-restraints excluded: chain R residue  148 ILE
Chi-restraints excluded: chain R residue  188 PHE
Chi-restraints excluded: chain R residue  253 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 103 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0870
   chunk 87 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
A 241 ASN
A 269 ASN
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.145966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.126224 restraints weight = 13978.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 2.57
r_work: 0.3495 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9055  Z= 0.175
  Angle     :  0.595  15.496  12256  Z= 0.305
  Chirality :  0.042   0.188   1399
  Planarity :  0.004   0.050   1524
  Dihedral  :  5.209  56.338   1271
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 26.67 %
    Favored  : 69.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.26), residues: 1104
  helix:  2.23 (0.24), residues: 416
  sheet: -0.55 (0.31), residues: 281
  loop : -0.95 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R  55 
 TYR   0.016   0.002   TYR S 178 
 PHE   0.023   0.002   PHE R  17 
 TRP   0.023   0.002   TRP A 211 
 HIS   0.005   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 9053)
  covalent geometry    : angle       0.59466 (12252)
  SS BOND              : bond        0.00327 (    2)
  SS BOND              : angle       0.72456 (    4)
  hydrogen bonds       : bond        0.04055 (  480)
  hydrogen bonds       : angle       4.42631 ( 1362)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 258
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 TRP cc_start: 0.7877 (p-90) cc_final: 0.7539 (p-90)
REVERT: A  267 PHE cc_start: 0.8516 (m-10) cc_final: 0.8201 (m-10)
REVERT: A  277 LYS cc_start: 0.8108 (ttmm) cc_final: 0.7804 (ttpt)
REVERT: A  341 ASP cc_start: 0.8009 (t0) cc_final: 0.7719 (t0)
REVERT: A  350 ASP cc_start: 0.7888 (t0) cc_final: 0.7483 (t0)
REVERT: B  189 SER cc_start: 0.8241 (t) cc_final: 0.7919 (p)
REVERT: C   21 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6498 (mpp)
REVERT: C   47 GLU cc_start: 0.6802 (mp0) cc_final: 0.6528 (mp0)
REVERT: S   59 TYR cc_start: 0.7100 (m-10) cc_final: 0.6833 (m-10)
REVERT: S   84 THR cc_start: 0.8152 (p) cc_final: 0.7881 (t)
REVERT: S  221 LEU cc_start: 0.8259 (mt) cc_final: 0.7975 (mt)
REVERT: R   16 GLU cc_start: 0.6963 (tm-30) cc_final: 0.6189 (tm-30)
REVERT: R  123 LYS cc_start: 0.6680 (OUTLIER) cc_final: 0.6113 (mmmt)
REVERT: R  212 MET cc_start: 0.7599 (mmm) cc_final: 0.7306 (mmp)
REVERT: R  270 MET cc_start: 0.5353 (ptm) cc_final: 0.5100 (ptm)
  outliers start: 42
  outliers final: 36
  residues processed: 281
  average time/residue: 0.0933
  time to fit residues: 36.2646
Evaluate side-chains
  296 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 258
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  222 GLU
Chi-restraints excluded: chain S residue  231 THR
Chi-restraints excluded: chain S residue  235 LEU
Chi-restraints excluded: chain R residue   44 VAL
Chi-restraints excluded: chain R residue   48 LEU
Chi-restraints excluded: chain R residue   60 TRP
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue  123 LYS
Chi-restraints excluded: chain R residue  148 ILE
Chi-restraints excluded: chain R residue  188 PHE
Chi-restraints excluded: chain R residue  253 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0170
   chunk 95 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 42 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 12 optimal weight:    0.1980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.4418

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

Flipped N/Q/H residues before XYZ refinement:
A 241 ASN
A 269 ASN
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.146057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.126375 restraints weight = 14015.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 2.57
r_work: 0.3493 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.125   9055  Z= 0.185
  Angle     :  0.919  59.198  12256  Z= 0.516
  Chirality :  0.043   0.319   1399
  Planarity :  0.004   0.049   1524
  Dihedral  :  5.242  56.617   1271
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.35 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 26.88 %
    Favored  : 68.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.26), residues: 1104
  helix:  2.27 (0.24), residues: 416
  sheet: -0.57 (0.31), residues: 281
  loop : -0.96 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R  55 
 TYR   0.015   0.002   TYR S 178 
 PHE   0.022   0.002   PHE S 227 
 TRP   0.016   0.002   TRP A 211 
 HIS   0.005   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 9053)
  covalent geometry    : angle       0.91883 (12252)
  SS BOND              : bond        0.00303 (    2)
  SS BOND              : angle       0.65008 (    4)
  hydrogen bonds       : bond        0.04043 (  480)
  hydrogen bonds       : angle       4.43024 ( 1362)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 258
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  216 GLU cc_start: 0.7391 (tt0) cc_final: 0.7089 (tm-30)
REVERT: A  267 PHE cc_start: 0.8507 (m-10) cc_final: 0.8185 (m-10)
REVERT: A  341 ASP cc_start: 0.8011 (t0) cc_final: 0.7727 (t0)
REVERT: A  350 ASP cc_start: 0.7878 (t0) cc_final: 0.7475 (t0)
REVERT: B  189 SER cc_start: 0.8245 (t) cc_final: 0.7902 (p)
REVERT: C   21 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6485 (mpp)
REVERT: C   47 GLU cc_start: 0.6782 (mp0) cc_final: 0.6509 (mp0)
REVERT: S   59 TYR cc_start: 0.7113 (m-10) cc_final: 0.6838 (m-10)
REVERT: S   84 THR cc_start: 0.8142 (p) cc_final: 0.7879 (t)
REVERT: S  221 LEU cc_start: 0.8256 (mt) cc_final: 0.7971 (mt)
REVERT: R   16 GLU cc_start: 0.6959 (tm-30) cc_final: 0.6190 (tm-30)
REVERT: R   58 LEU cc_start: 0.7703 (tp) cc_final: 0.7433 (tt)
REVERT: R  123 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.6118 (mmmt)
REVERT: R  212 MET cc_start: 0.7587 (mmm) cc_final: 0.7295 (mmp)
REVERT: R  270 MET cc_start: 0.5338 (ptm) cc_final: 0.5081 (ptm)
  outliers start: 43
  outliers final: 39
  residues processed: 283
  average time/residue: 0.0954
  time to fit residues: 37.3259
Evaluate side-chains
  305 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 264
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  174 GLN
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  222 GLU
Chi-restraints excluded: chain S residue  231 THR
Chi-restraints excluded: chain S residue  235 LEU
Chi-restraints excluded: chain R residue   44 VAL
Chi-restraints excluded: chain R residue   48 LEU
Chi-restraints excluded: chain R residue   60 TRP
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue  110 LYS
Chi-restraints excluded: chain R residue  123 LYS
Chi-restraints excluded: chain R residue  148 ILE
Chi-restraints excluded: chain R residue  188 PHE
Chi-restraints excluded: chain R residue  253 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 98 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 61 optimal weight:    0.4980
   chunk 81 optimal weight:    1.9990
   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 241 ASN
A 269 ASN
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.146131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.126784 restraints weight = 13920.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 2.53
r_work: 0.3500 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
moved from start:          0.1935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.119   9055  Z= 0.192
  Angle     :  0.839  47.328  12256  Z= 0.465
  Chirality :  0.042   0.263   1399
  Planarity :  0.004   0.049   1524
  Dihedral  :  5.242  56.617   1271
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.35 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 27.19 %
    Favored  : 68.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.26), residues: 1104
  helix:  2.27 (0.24), residues: 416
  sheet: -0.57 (0.31), residues: 281
  loop : -0.96 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R  55 
 TYR   0.015   0.002   TYR S 178 
 PHE   0.022   0.002   PHE S 227 
 TRP   0.016   0.002   TRP A 211 
 HIS   0.005   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 9053)
  covalent geometry    : angle       0.83866 (12252)
  SS BOND              : bond        0.00303 (    2)
  SS BOND              : angle       0.65008 (    4)
  hydrogen bonds       : bond        0.04043 (  480)
  hydrogen bonds       : angle       4.43024 ( 1362)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2044.93 seconds
wall clock time: 36 minutes 3.83 seconds (2163.83 seconds total)