Starting phenix.real_space_refine
on Wed Sep 17 12:11:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yw4_39622/09_2025/8yw4_39622.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yw4_39622/09_2025/8yw4_39622.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yw4_39622/09_2025/8yw4_39622.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yw4_39622/09_2025/8yw4_39622.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yw4_39622/09_2025/8yw4_39622.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yw4_39622/09_2025/8yw4_39622.cif"
  }
  resolution = 3.26
  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=   0.037
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    5466      2.51       5
     N    1522      2.21       5
     O    1583      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  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: 8619
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1950
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2614
          Classifications: {'peptide': 341}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 983
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 983
          Classifications: {'peptide': 129}
          Link IDs: {'PTRANS': 5, 'TRANS': 123}
    Chain: "R"
      Number of atoms: 2416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2416
          Classifications: {'peptide': 293}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 8, 'TRANS': 284}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "P"
      Number of atoms: 220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 220
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Planarities with less than four sites: {'AIB:plan-1': 2, '2ML:plan-1': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 2.36, per 1000 atoms: 0.27
  Number of scatterers: 8619
  At special positions: 0
  Unit cell: (84.609, 100.674, 162.792, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    1583      8.00
     N    1522      7.00
     C    5466      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 216 " - pdb=" SG  CYS R 286 " 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: 0.76
  Conformation dependent library (CDL) restraints added in 467.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2026

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 11 sheets defined
      43.7% alpha, 15.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 33
      removed outlier: 3.722A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.717A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 216
      removed outlier: 3.679A  pdb=" N   ASN A 216 " --> pdb=" O   GLN A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 246
    Processing helix  chain 'A' and resid 260 through 271
      removed outlier: 3.598A  pdb=" N   LEU A 264 " --> pdb=" O   LYS A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 278
    Processing helix  chain 'A' and resid 298 through 320
      removed outlier: 3.578A  pdb=" N   ILE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ILE A 315 " --> pdb=" O   GLU A 311 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   SER A 319 " --> pdb=" O   ILE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 358
      removed outlier: 3.882A  pdb=" N   ASP A 348 " --> pdb=" O   ASN A 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.577A  pdb=" N   GLU B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 3.662A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.875A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 32 through 48
      removed outlier: 3.689A  pdb=" N   TYR R  36 " --> pdb=" O   ALA R  32 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLN R  37 " --> pdb=" O   GLY R  33 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG R  41 " --> pdb=" O   GLN R  37 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ARG R  43 " --> pdb=" O   TRP R  39 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLU R  45 " --> pdb=" O   ARG R  41 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 128 through 161
      removed outlier: 3.512A  pdb=" N   LEU R 153 " --> pdb=" O   LEU R 149 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LEU R 154 " --> pdb=" O   ALA R 150 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 167 through 194
    Processing helix  chain 'R' and resid 196 through 201
      removed outlier: 3.891A  pdb=" N   TYR R 200 " --> pdb=" O   ARG R 196 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 212 through 246
      removed outlier: 3.501A  pdb=" N   LEU R 235 " --> pdb=" O   TYR R 231 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 255 through 265
    Processing helix  chain 'R' and resid 265 through 282
      removed outlier: 3.674A  pdb=" N   LEU R 269 " --> pdb=" O   GLY R 265 " (cutoff:3.500A)
      Proline residue:  R 273  - end of helix
    Processing helix  chain 'R' and resid 292 through 297
      removed outlier: 3.537A  pdb=" N   TRP R 296 " --> pdb=" O   VAL R 292 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   TRP R 297 " --> pdb=" O   LYS R 293 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 292 through 297'
    Processing helix  chain 'R' and resid 299 through 328
      removed outlier: 3.677A  pdb=" N   ILE R 303 " --> pdb=" O   ILE R 299 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ARG R 328 " --> pdb=" O   LYS R 324 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 335 through 351
      Proline residue:  R 348  - end of helix
    Processing helix  chain 'R' and resid 352 through 358
      removed outlier: 3.546A  pdb=" N   VAL R 356 " --> pdb=" O   HIS R 353 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA R 358 " --> pdb=" O   VAL R 355 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 367 through 392
      removed outlier: 3.886A  pdb=" N   PHE R 371 " --> pdb=" O   GLY R 367 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   GLY R 385 " --> pdb=" O   SER R 381 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   PHE R 386 " --> pdb=" O   SER R 382 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 396 through 411
      removed outlier: 3.947A  pdb=" N   ARG R 404 " --> pdb=" O   GLN R 400 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 2 through 27
      removed outlier: 3.513A  pdb=" N   ILE P  12 " --> pdb=" O   SER P   8 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ASP P  15 " --> pdb=" O   SER P  11 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LYS P  17 " --> pdb=" O   2ML P  13 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   GLU P  24 " --> pdb=" O   AIB P  20 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU P  27 " --> pdb=" O   ILE P  23 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191
      removed outlier: 4.860A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.960A  pdb=" N   ILE A 222 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 8.293A  pdb=" N   ASP A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   PHE A 257 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ASN A 259 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.084A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.613A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 3.503A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105
      removed outlier: 3.548A  pdb=" N   ALA B 104 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 5.865A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 150
      removed outlier: 4.248A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   CYS B 166 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.341A  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: 6.788A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232
      removed outlier: 3.679A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.918A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.709A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.629A  pdb=" N   LEU B 285 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 10 through 12
      removed outlier: 5.992A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 17 through 23
      removed outlier: 3.687A  pdb=" N   LEU N  18 " --> pdb=" O   MET N  83 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60

    423 hydrogen bonds defined for protein.
    1194 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: 1.48

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2532
        1.33 -     1.45: 1521
        1.45 -     1.57: 4675
        1.57 -     1.69: 1
        1.69 -     1.81: 66
  Bond restraints: 8795
  Sorted by residual:
  bond pdb=" N   GLY R 198 "
       pdb=" CA  GLY R 198 "
    ideal  model  delta    sigma   weight residual
    1.444  1.475 -0.031 8.80e-03 1.29e+04 1.24e+01
  bond pdb=" CA  2ML P  13 "
       pdb=" C   2ML P  13 "
    ideal  model  delta    sigma   weight residual
    1.525  1.578 -0.053 2.10e-02 2.27e+03 6.26e+00
  bond pdb=" N   ASP B  38 "
       pdb=" CA  ASP B  38 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.45e-02 4.76e+03 6.13e+00
  bond pdb=" N   AIB P  20 "
       pdb=" CA  AIB P  20 "
    ideal  model  delta    sigma   weight residual
    1.458  1.500 -0.042 1.90e-02 2.77e+03 4.96e+00
  bond pdb=" N   AIB P   2 "
       pdb=" CA  AIB P   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.499 -0.041 1.90e-02 2.77e+03 4.60e+00
  ... (remaining 8790 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 11721
        1.89 -     3.79: 159
        3.79 -     5.68: 21
        5.68 -     7.58: 5
        7.58 -     9.47: 3
  Bond angle restraints: 11909
  Sorted by residual:
  angle pdb=" O   GLY R 198 "
        pdb=" C   GLY R 198 "
        pdb=" N   PRO R 199 "
      ideal   model   delta    sigma   weight residual
     121.07  122.28   -1.21 3.60e-01 7.72e+00 1.13e+01
  angle pdb=" N   PHE A 282 "
        pdb=" CA  PHE A 282 "
        pdb=" C   PHE A 282 "
      ideal   model   delta    sigma   weight residual
     114.56  110.45    4.11 1.27e+00 6.20e-01 1.05e+01
  angle pdb=" N   GLY R 198 "
        pdb=" CA  GLY R 198 "
        pdb=" C   GLY R 198 "
      ideal   model   delta    sigma   weight residual
     115.22  111.58    3.64 1.27e+00 6.20e-01 8.21e+00
  angle pdb=" CA  LEU R 261 "
        pdb=" CB  LEU R 261 "
        pdb=" CG  LEU R 261 "
      ideal   model   delta    sigma   weight residual
     116.30  125.77   -9.47 3.50e+00 8.16e-02 7.32e+00
  angle pdb=" N   PRO R 199 "
        pdb=" CA  PRO R 199 "
        pdb=" C   PRO R 199 "
      ideal   model   delta    sigma   weight residual
     113.81  109.90    3.91 1.45e+00 4.76e-01 7.28e+00
  ... (remaining 11904 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 4370
       17.59 -    35.19: 600
       35.19 -    52.78: 201
       52.78 -    70.37: 40
       70.37 -    87.97: 10
  Dihedral angle restraints: 5221
    sinusoidal: 2080
      harmonic: 3141
  Sorted by residual:
  dihedral pdb=" CB  CYS R 216 "
           pdb=" SG  CYS R 216 "
           pdb=" SG  CYS R 286 "
           pdb=" CB  CYS R 286 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   24.50   68.50     1      1.00e+01 1.00e-02 6.08e+01
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   62.74   30.26     1      1.00e+01 1.00e-02 1.31e+01
  dihedral pdb=" CA  ASP R 129 "
           pdb=" CB  ASP R 129 "
           pdb=" CG  ASP R 129 "
           pdb=" OD1 ASP R 129 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.93   58.93     1      2.00e+01 2.50e-03 1.16e+01
  ... (remaining 5218 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1105
       0.051 -    0.102: 181
       0.102 -    0.153: 36
       0.153 -    0.204: 0
       0.204 -    0.255: 2
  Chirality restraints: 1324
  Sorted by residual:
  chirality pdb=" CA  2ML P  13 "
            pdb=" C   2ML P  13 "
            pdb=" CB1 2ML P  13 "
            pdb=" CB2 2ML P  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.84   -3.10    0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CB  THR B 181 "
            pdb=" CA  THR B 181 "
            pdb=" OG1 THR B 181 "
            pdb=" CG2 THR B 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CG  LEU R 182 "
            pdb=" CB  LEU R 182 "
            pdb=" CD1 LEU R 182 "
            pdb=" CD2 LEU R 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.15 2.00e-01 2.50e+01 5.53e-01
  ... (remaining 1321 not shown)

  Planarity restraints: 1518
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN G  59 "   -0.039 5.00e-02 4.00e+02   6.06e-02 5.88e+00
        pdb=" N   PRO G  60 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO G  60 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO G  60 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.028 5.00e-02 4.00e+02   4.32e-02 2.98e+00
        pdb=" N   PRO B 236 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  38 "   -0.027 5.00e-02 4.00e+02   4.10e-02 2.69e+00
        pdb=" N   PRO B  39 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO B  39 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B  39 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1515 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 531
        2.73 -     3.27: 8572
        3.27 -     3.82: 14119
        3.82 -     4.36: 16719
        4.36 -     4.90: 29320
  Nonbonded interactions: 69261
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 205 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.190 3.120
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OD1 ASP B 228 "
            pdb=" OH  TYR N 117 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OG1 THR N 104 "
            pdb=" OD1 ASP N 106 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OH  TYR R 225 "
            pdb=" O   TRP R 264 "
     model   vdw
     2.249 3.040
  ... (remaining 69256 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:             1.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.000
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6493
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   0.053   8797  Z= 0.177
  Angle     :  0.561   9.472  11913  Z= 0.296
  Chirality :  0.040   0.255   1324
  Planarity :  0.003   0.061   1518
  Dihedral  : 18.345  87.967   3189
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.22 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 33.88 %
    Favored  : 65.80 %
  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: -0.25 (0.27), residues: 1054
  helix:  1.23 (0.25), residues: 406
  sheet: -1.13 (0.36), residues: 222
  loop : -0.91 (0.32), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N 105 
 TYR   0.015   0.001   TYR R 335 
 PHE   0.024   0.001   PHE R 379 
 TRP   0.010   0.001   TRP A 211 
 HIS   0.002   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 8795)
  covalent geometry    : angle       0.56123 (11909)
  SS BOND              : bond        0.00122 (    2)
  SS BOND              : angle       0.53701 (    4)
  hydrogen bonds       : bond        0.25590 (  423)
  hydrogen bonds       : angle       7.49223 ( 1194)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 212
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: B  262 MET cc_start: 0.6332 (mtp) cc_final: 0.6115 (ttm)
REVERT: N   94 TYR cc_start: 0.6910 (m-80) cc_final: 0.5990 (m-80)
REVERT: R  297 TRP cc_start: 0.7098 (m100) cc_final: 0.5926 (m-10)
  outliers start: 3
  outliers final: 0
  residues processed: 212
  average time/residue: 0.1256
  time to fit residues: 34.2494
Evaluate side-chains
  132 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    0.0980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.1980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
R 173 HIS
** R 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 409 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.169255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.121026 restraints weight = 10374.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 2.79
r_work: 0.3255 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.3122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8797  Z= 0.170
  Angle     :  0.664  13.266  11913  Z= 0.342
  Chirality :  0.043   0.143   1324
  Planarity :  0.005   0.040   1518
  Dihedral  :  4.248  37.095   1199
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.46 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  6.19 %
    Allowed  : 28.34 %
    Favored  : 65.47 %
  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:  0.17 (0.27), residues: 1054
  helix:  1.64 (0.24), residues: 415
  sheet: -1.25 (0.35), residues: 223
  loop : -0.56 (0.33), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 232 
 TYR   0.016   0.002   TYR R 335 
 PHE   0.018   0.002   PHE R 177 
 TRP   0.027   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 8795)
  covalent geometry    : angle       0.66429 (11909)
  SS BOND              : bond        0.00377 (    2)
  SS BOND              : angle       0.89670 (    4)
  hydrogen bonds       : bond        0.05101 (  423)
  hydrogen bonds       : angle       4.75473 ( 1194)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 158
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7133 (tmm)
REVERT: B   13 GLN cc_start: 0.8197 (tp40) cc_final: 0.7974 (tm-30)
REVERT: B   87 THR cc_start: 0.8340 (m) cc_final: 0.8071 (m)
REVERT: B  226 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8205 (pt0)
REVERT: B  262 MET cc_start: 0.7513 (mtp) cc_final: 0.7265 (ttm)
REVERT: B  338 ILE cc_start: 0.8001 (mt) cc_final: 0.7572 (mt)
REVERT: N   71 SER cc_start: 0.6818 (OUTLIER) cc_final: 0.6605 (p)
REVERT: N   89 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7210 (pm20)
REVERT: R  140 MET cc_start: 0.8123 (tmm) cc_final: 0.7778 (tmm)
REVERT: R  181 MET cc_start: 0.7039 (OUTLIER) cc_final: 0.6733 (ttm)
REVERT: R  182 LEU cc_start: 0.6953 (tt) cc_final: 0.6752 (tt)
REVERT: R  297 TRP cc_start: 0.7455 (m100) cc_final: 0.6119 (m-10)
  outliers start: 57
  outliers final: 21
  residues processed: 196
  average time/residue: 0.0957
  time to fit residues: 25.7627
Evaluate side-chains
  166 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 140
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  287 THR
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  331 THR
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue   36 TYR
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  167 CYS
Chi-restraints excluded: chain R residue  181 MET
Chi-restraints excluded: chain R residue  188 LEU
Chi-restraints excluded: chain R residue  189 SER
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain R residue  325 LEU
Chi-restraints excluded: chain R residue  381 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 63 optimal weight:    6.9990
   chunk 92 optimal weight:    1.9990
   chunk 16 optimal weight:    9.9990
   chunk 15 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 4 optimal weight:    0.2980
   chunk 26 optimal weight:    0.0470
   chunk 32 optimal weight:    0.1980
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN
A 259 ASN
B  17 GLN
B 175 GLN
R 285 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.169222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.121882 restraints weight = 10382.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 2.78
r_work: 0.3271 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.4356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8797  Z= 0.136
  Angle     :  0.554   8.868  11913  Z= 0.287
  Chirality :  0.041   0.171   1324
  Planarity :  0.004   0.069   1518
  Dihedral  :  4.007  52.826   1199
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.27 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 28.88 %
    Favored  : 65.36 %
  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:  0.60 (0.27), residues: 1054
  helix:  2.22 (0.25), residues: 409
  sheet: -1.01 (0.35), residues: 230
  loop : -0.54 (0.33), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 256 
 TYR   0.022   0.001   TYR R 281 
 PHE   0.026   0.002   PHE A 343 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.003   0.001   HIS R 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 8795)
  covalent geometry    : angle       0.55362 (11909)
  SS BOND              : bond        0.00142 (    2)
  SS BOND              : angle       0.82303 (    4)
  hydrogen bonds       : bond        0.04787 (  423)
  hydrogen bonds       : angle       4.37308 ( 1194)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 154
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 GLN cc_start: 0.8066 (tp40) cc_final: 0.7398 (tp-100)
REVERT: A  198 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7481 (tmm)
REVERT: A  345 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8134 (t0)
REVERT: B   87 THR cc_start: 0.8420 (m) cc_final: 0.8169 (m)
REVERT: B  338 ILE cc_start: 0.8307 (mt) cc_final: 0.7858 (mt)
REVERT: R  140 MET cc_start: 0.8183 (tmm) cc_final: 0.7872 (tmm)
REVERT: R  154 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6660 (tt)
REVERT: R  164 ARG cc_start: 0.5066 (mtt180) cc_final: 0.4380 (mmt180)
REVERT: R  181 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7280 (ttm)
REVERT: R  321 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7689 (tt)
  outliers start: 53
  outliers final: 30
  residues processed: 186
  average time/residue: 0.0946
  time to fit residues: 23.7540
Evaluate side-chains
  174 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 139
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain A residue  346 CYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  134 LEU
Chi-restraints excluded: chain R residue  146 SER
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  167 CYS
Chi-restraints excluded: chain R residue  180 PHE
Chi-restraints excluded: chain R residue  181 MET
Chi-restraints excluded: chain R residue  188 LEU
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  299 ILE
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain R residue  381 SER
Chi-restraints excluded: chain P residue   14 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 99 optimal weight:    9.9990
   chunk 65 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 44 optimal weight:    0.3980
   chunk 37 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 173 HIS
R 285 GLN

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 = 0.164398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.116108 restraints weight = 10545.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.50
r_work: 0.3155 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.6903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   8797  Z= 0.230
  Angle     :  0.713  10.207  11913  Z= 0.370
  Chirality :  0.046   0.228   1324
  Planarity :  0.005   0.046   1518
  Dihedral  :  4.660  43.521   1199
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.79 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 28.88 %
    Favored  : 65.04 %
  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:  0.36 (0.27), residues: 1054
  helix:  1.97 (0.25), residues: 409
  sheet: -1.11 (0.35), residues: 229
  loop : -0.64 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 314 
 TYR   0.016   0.002   TYR A 306 
 PHE   0.019   0.002   PHE B 241 
 TRP   0.017   0.002   TRP N  47 
 HIS   0.006   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 ( 8795)
  covalent geometry    : angle       0.71299 (11909)
  SS BOND              : bond        0.00245 (    2)
  SS BOND              : angle       0.66883 (    4)
  hydrogen bonds       : bond        0.04911 (  423)
  hydrogen bonds       : angle       4.56654 ( 1194)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 164
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A  345 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8457 (t70)
REVERT: A  353 MET cc_start: 0.7874 (ttm) cc_final: 0.7635 (ttm)
REVERT: B   17 GLN cc_start: 0.8287 (tp-100) cc_final: 0.7690 (tt0)
REVERT: B   59 TYR cc_start: 0.9093 (OUTLIER) cc_final: 0.8199 (m-80)
REVERT: B   87 THR cc_start: 0.8897 (m) cc_final: 0.8695 (m)
REVERT: B  172 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7954 (mm-30)
REVERT: B  267 ASP cc_start: 0.8433 (m-30) cc_final: 0.8047 (p0)
REVERT: G   13 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7488 (ptp90)
REVERT: N   89 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7435 (pm20)
REVERT: N  105 ARG cc_start: 0.8321 (mpp80) cc_final: 0.7996 (ptp90)
REVERT: N  118 ARG cc_start: 0.8183 (mtm110) cc_final: 0.7929 (mtm-85)
REVERT: R  140 MET cc_start: 0.8319 (tmm) cc_final: 0.8044 (tmm)
REVERT: R  164 ARG cc_start: 0.5389 (mtt180) cc_final: 0.4382 (mmt180)
REVERT: R  165 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7333 (mt)
REVERT: R  181 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7719 (ttm)
REVERT: R  288 GLU cc_start: 0.7284 (tt0) cc_final: 0.7044 (tm-30)
REVERT: R  297 TRP cc_start: 0.7804 (m100) cc_final: 0.6254 (m-10)
  outliers start: 56
  outliers final: 32
  residues processed: 206
  average time/residue: 0.0980
  time to fit residues: 27.5069
Evaluate side-chains
  187 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 149
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  287 THR
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  331 THR
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain G residue   13 ARG
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  146 SER
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  167 CYS
Chi-restraints excluded: chain R residue  180 PHE
Chi-restraints excluded: chain R residue  181 MET
Chi-restraints excluded: chain R residue  189 SER
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  381 SER
Chi-restraints excluded: chain P residue   14 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 99 optimal weight:    6.9990
   chunk 73 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 190 GLN
** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN
B 175 GLN
R 285 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.163187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.122477 restraints weight = 9977.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 1.97
r_work: 0.3100 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.7316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8797  Z= 0.176
  Angle     :  0.580  10.713  11913  Z= 0.298
  Chirality :  0.042   0.163   1324
  Planarity :  0.004   0.042   1518
  Dihedral  :  4.275  45.292   1199
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.74 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 30.40 %
    Favored  : 64.50 %
  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:  0.40 (0.27), residues: 1054
  helix:  2.07 (0.25), residues: 410
  sheet: -1.07 (0.35), residues: 225
  loop : -0.74 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 247 
 TYR   0.013   0.001   TYR R 141 
 PHE   0.016   0.002   PHE A 343 
 TRP   0.017   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 8795)
  covalent geometry    : angle       0.58027 (11909)
  SS BOND              : bond        0.00134 (    2)
  SS BOND              : angle       0.90943 (    4)
  hydrogen bonds       : bond        0.04193 (  423)
  hydrogen bonds       : angle       4.28849 ( 1194)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 166
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   46 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7077 (mtp85)
REVERT: B   78 LYS cc_start: 0.8604 (tppt) cc_final: 0.8370 (tptt)
REVERT: B   87 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.8913 (m)
REVERT: G   18 GLN cc_start: 0.8590 (tp-100) cc_final: 0.8357 (tp40)
REVERT: N  105 ARG cc_start: 0.8207 (mpp80) cc_final: 0.7937 (ptp-170)
REVERT: R  164 ARG cc_start: 0.5548 (mtt180) cc_final: 0.4527 (mmt180)
REVERT: R  165 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7592 (mt)
  outliers start: 47
  outliers final: 30
  residues processed: 197
  average time/residue: 0.1026
  time to fit residues: 27.3118
Evaluate side-chains
  190 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 157
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  134 LEU
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  167 CYS
Chi-restraints excluded: chain R residue  180 PHE
Chi-restraints excluded: chain R residue  284 THR
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain R residue  318 LEU
Chi-restraints excluded: chain R residue  325 LEU
Chi-restraints excluded: chain P residue   14 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 75 optimal weight:   10.0000
   chunk 42 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 100 optimal weight:    4.9990
   chunk 99 optimal weight:    6.9990
   chunk 92 optimal weight:    0.5980
   chunk 70 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 175 GLN
R 285 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.162618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.121941 restraints weight = 9965.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.08
r_work: 0.3002 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.7691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8797  Z= 0.168
  Angle     :  0.566   7.897  11913  Z= 0.293
  Chirality :  0.042   0.210   1324
  Planarity :  0.004   0.042   1518
  Dihedral  :  4.266  47.658   1199
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.31 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 30.40 %
    Favored  : 64.06 %
  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:  0.47 (0.27), residues: 1054
  helix:  2.15 (0.25), residues: 415
  sheet: -1.04 (0.34), residues: 231
  loop : -0.74 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 289 
 TYR   0.012   0.001   TYR N  60 
 PHE   0.015   0.001   PHE B 199 
 TRP   0.017   0.001   TRP R 287 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 8795)
  covalent geometry    : angle       0.56588 (11909)
  SS BOND              : bond        0.00061 (    2)
  SS BOND              : angle       0.69925 (    4)
  hydrogen bonds       : bond        0.04072 (  423)
  hydrogen bonds       : angle       4.22422 ( 1194)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 177
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   45 MET cc_start: 0.8977 (mtt) cc_final: 0.8482 (mtt)
REVERT: B   87 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.9011 (m)
REVERT: G   18 GLN cc_start: 0.8366 (tp-100) cc_final: 0.8085 (tp40)
REVERT: N  105 ARG cc_start: 0.8280 (mpp80) cc_final: 0.8011 (ptp-170)
REVERT: R  164 ARG cc_start: 0.5669 (mtt180) cc_final: 0.4848 (mmt180)
REVERT: R  165 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7426 (mt)
REVERT: R  166 HIS cc_start: 0.7717 (OUTLIER) cc_final: 0.7445 (m-70)
REVERT: R  290 ASN cc_start: 0.7436 (m-40) cc_final: 0.7203 (m110)
  outliers start: 51
  outliers final: 35
  residues processed: 211
  average time/residue: 0.1001
  time to fit residues: 28.8059
Evaluate side-chains
  210 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 172
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  132 LEU
Chi-restraints excluded: chain R residue  134 LEU
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  146 SER
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  166 HIS
Chi-restraints excluded: chain R residue  167 CYS
Chi-restraints excluded: chain R residue  180 PHE
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  189 SER
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain R residue  318 LEU
Chi-restraints excluded: chain R residue  325 LEU
Chi-restraints excluded: chain R residue  381 SER
Chi-restraints excluded: chain P residue   14 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 74 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
R 173 HIS
R 285 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.163649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.122111 restraints weight = 10014.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.14
r_work: 0.3008 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.8010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8797  Z= 0.142
  Angle     :  0.546   9.973  11913  Z= 0.281
  Chirality :  0.041   0.205   1324
  Planarity :  0.004   0.076   1518
  Dihedral  :  4.075  45.432   1199
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.84 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 31.49 %
    Favored  : 63.74 %
  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:  0.58 (0.27), residues: 1054
  helix:  2.33 (0.26), residues: 415
  sheet: -1.04 (0.34), residues: 231
  loop : -0.74 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 232 
 TYR   0.027   0.001   TYR R 281 
 PHE   0.022   0.002   PHE P   6 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 8795)
  covalent geometry    : angle       0.54607 (11909)
  SS BOND              : bond        0.00046 (    2)
  SS BOND              : angle       0.74718 (    4)
  hydrogen bonds       : bond        0.03782 (  423)
  hydrogen bonds       : angle       4.10689 ( 1194)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 176
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: B   45 MET cc_start: 0.9102 (mtt) cc_final: 0.8627 (mtt)
REVERT: B   87 THR cc_start: 0.9269 (OUTLIER) cc_final: 0.9039 (m)
REVERT: G   18 GLN cc_start: 0.8321 (tp-100) cc_final: 0.7980 (tp40)
REVERT: G   62 ARG cc_start: 0.7576 (tpp-160) cc_final: 0.7182 (mmp80)
REVERT: N   72 ARG cc_start: 0.9036 (ptm160) cc_final: 0.8822 (ptm160)
REVERT: N  105 ARG cc_start: 0.8284 (mpp80) cc_final: 0.8041 (ptp-170)
REVERT: R  147 LEU cc_start: 0.8619 (tp) cc_final: 0.8376 (tt)
REVERT: R  164 ARG cc_start: 0.5462 (mtt180) cc_final: 0.4768 (mmt180)
REVERT: R  165 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7466 (mt)
REVERT: R  290 ASN cc_start: 0.7390 (m-40) cc_final: 0.7046 (m110)
  outliers start: 44
  outliers final: 29
  residues processed: 207
  average time/residue: 0.0969
  time to fit residues: 27.3025
Evaluate side-chains
  203 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 172
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  132 LEU
Chi-restraints excluded: chain R residue  134 LEU
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  167 CYS
Chi-restraints excluded: chain R residue  180 PHE
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  188 LEU
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain R residue  318 LEU
Chi-restraints excluded: chain R residue  325 LEU
Chi-restraints excluded: chain P residue   14 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 35 optimal weight:    0.0770
   chunk 96 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 39 optimal weight:    0.2980
   chunk 15 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 68 optimal weight:    0.0170
   chunk 55 optimal weight:    0.8980
   chunk 97 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.3576

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
G  59 ASN
R 285 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.166073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.124362 restraints weight = 9818.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.89
r_work: 0.3192 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.8136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8797  Z= 0.106
  Angle     :  0.520   9.451  11913  Z= 0.270
  Chirality :  0.040   0.236   1324
  Planarity :  0.004   0.066   1518
  Dihedral  :  3.945  44.650   1199
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.31 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 31.81 %
    Favored  : 63.84 %
  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:  0.71 (0.27), residues: 1054
  helix:  2.45 (0.26), residues: 414
  sheet: -0.91 (0.34), residues: 228
  loop : -0.74 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 232 
 TYR   0.019   0.001   TYR R 281 
 PHE   0.013   0.001   PHE R 357 
 TRP   0.019   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 8795)
  covalent geometry    : angle       0.52007 (11909)
  SS BOND              : bond        0.00093 (    2)
  SS BOND              : angle       0.56167 (    4)
  hydrogen bonds       : bond        0.03436 (  423)
  hydrogen bonds       : angle       3.99264 ( 1194)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 179
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: B   45 MET cc_start: 0.8886 (mtt) cc_final: 0.8426 (mtt)
REVERT: B   46 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7056 (mtp85)
REVERT: B   87 THR cc_start: 0.9281 (OUTLIER) cc_final: 0.8997 (m)
REVERT: G   18 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8422 (tp-100)
REVERT: G   62 ARG cc_start: 0.7537 (tpp-160) cc_final: 0.7191 (mmp80)
REVERT: R  147 LEU cc_start: 0.8664 (tp) cc_final: 0.8415 (tt)
REVERT: R  152 LEU cc_start: 0.8294 (tt) cc_final: 0.7994 (tt)
REVERT: R  165 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7557 (mt)
REVERT: R  290 ASN cc_start: 0.7295 (m-40) cc_final: 0.6907 (m110)
  outliers start: 40
  outliers final: 31
  residues processed: 205
  average time/residue: 0.1027
  time to fit residues: 28.3989
Evaluate side-chains
  205 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 171
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  132 LEU
Chi-restraints excluded: chain R residue  134 LEU
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  166 HIS
Chi-restraints excluded: chain R residue  167 CYS
Chi-restraints excluded: chain R residue  173 HIS
Chi-restraints excluded: chain R residue  180 PHE
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  188 LEU
Chi-restraints excluded: chain R residue  189 SER
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain R residue  318 LEU
Chi-restraints excluded: chain R residue  325 LEU
Chi-restraints excluded: chain P residue   14 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 77 optimal weight:    0.6980
   chunk 103 optimal weight:    7.9990
   chunk 43 optimal weight:    1.9990
   chunk 63 optimal weight:    0.4980
   chunk 3 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
R 285 GLN
R 364 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.161144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.108651 restraints weight = 10354.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.49
r_work: 0.3109 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.8259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8797  Z= 0.152
  Angle     :  0.558   9.599  11913  Z= 0.287
  Chirality :  0.042   0.213   1324
  Planarity :  0.004   0.073   1518
  Dihedral  :  4.024  44.298   1199
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.12 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 32.36 %
    Favored  : 63.74 %
  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:  0.63 (0.27), residues: 1054
  helix:  2.40 (0.26), residues: 416
  sheet: -1.02 (0.34), residues: 231
  loop : -0.77 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N  72 
 TYR   0.020   0.001   TYR R 281 
 PHE   0.024   0.002   PHE P   6 
 TRP   0.015   0.001   TRP R 297 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 8795)
  covalent geometry    : angle       0.55823 (11909)
  SS BOND              : bond        0.00129 (    2)
  SS BOND              : angle       0.71606 (    4)
  hydrogen bonds       : bond        0.03708 (  423)
  hydrogen bonds       : angle       4.00846 ( 1194)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 169
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
REVERT: B   45 MET cc_start: 0.9297 (mtt) cc_final: 0.8866 (mtt)
REVERT: B   87 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.9005 (m)
REVERT: G   18 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7855 (tp-100)
REVERT: G   62 ARG cc_start: 0.7544 (tpp-160) cc_final: 0.7191 (mmp80)
REVERT: R  147 LEU cc_start: 0.8454 (tp) cc_final: 0.8251 (tt)
REVERT: R  152 LEU cc_start: 0.8036 (tt) cc_final: 0.7621 (tt)
REVERT: R  290 ASN cc_start: 0.7389 (m-40) cc_final: 0.7048 (m110)
  outliers start: 36
  outliers final: 31
  residues processed: 194
  average time/residue: 0.0956
  time to fit residues: 25.5510
Evaluate side-chains
  198 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 166
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  132 LEU
Chi-restraints excluded: chain R residue  134 LEU
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  166 HIS
Chi-restraints excluded: chain R residue  167 CYS
Chi-restraints excluded: chain R residue  173 HIS
Chi-restraints excluded: chain R residue  180 PHE
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  189 SER
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain R residue  318 LEU
Chi-restraints excluded: chain R residue  325 LEU
Chi-restraints excluded: chain P residue   14 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 57 optimal weight:    7.9990
   chunk 33 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 86 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
B  54 HIS
R 285 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.161543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.109137 restraints weight = 10392.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 2.46
r_work: 0.3118 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.8437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8797  Z= 0.143
  Angle     :  0.552   9.505  11913  Z= 0.284
  Chirality :  0.042   0.213   1324
  Planarity :  0.004   0.072   1518
  Dihedral  :  4.009  43.213   1199
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.22 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 32.14 %
    Favored  : 63.74 %
  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:  0.62 (0.27), residues: 1054
  helix:  2.41 (0.26), residues: 416
  sheet: -1.03 (0.34), residues: 231
  loop : -0.80 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N  72 
 TYR   0.020   0.001   TYR R 281 
 PHE   0.014   0.001   PHE B 199 
 TRP   0.015   0.001   TRP R 297 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8795)
  covalent geometry    : angle       0.55156 (11909)
  SS BOND              : bond        0.00190 (    2)
  SS BOND              : angle       0.81073 (    4)
  hydrogen bonds       : bond        0.03624 (  423)
  hydrogen bonds       : angle       3.99833 ( 1194)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 170
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: B   45 MET cc_start: 0.9317 (mtt) cc_final: 0.8911 (mtt)
REVERT: B   87 THR cc_start: 0.9207 (OUTLIER) cc_final: 0.8981 (m)
REVERT: G   18 GLN cc_start: 0.8083 (tp-100) cc_final: 0.7878 (tp-100)
REVERT: G   62 ARG cc_start: 0.7567 (tpp-160) cc_final: 0.7249 (mmp80)
REVERT: N   53 GLN cc_start: 0.7933 (mp10) cc_final: 0.7718 (mp10)
REVERT: R  147 LEU cc_start: 0.8488 (tp) cc_final: 0.8275 (tt)
REVERT: R  152 LEU cc_start: 0.8095 (tt) cc_final: 0.7703 (tt)
REVERT: R  290 ASN cc_start: 0.7372 (m-40) cc_final: 0.7003 (m110)
  outliers start: 38
  outliers final: 31
  residues processed: 197
  average time/residue: 0.0958
  time to fit residues: 25.7516
Evaluate side-chains
  198 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 166
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  132 LEU
Chi-restraints excluded: chain R residue  134 LEU
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  166 HIS
Chi-restraints excluded: chain R residue  167 CYS
Chi-restraints excluded: chain R residue  173 HIS
Chi-restraints excluded: chain R residue  180 PHE
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  189 SER
Chi-restraints excluded: chain R residue  239 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain R residue  318 LEU
Chi-restraints excluded: chain R residue  325 LEU
Chi-restraints excluded: chain P residue   14 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 50 optimal weight:    0.3980
   chunk 66 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN
B  13 GLN
B  17 GLN
R 285 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.162161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.109532 restraints weight = 10334.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.50
r_work: 0.3116 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.8539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8797  Z= 0.131
  Angle     :  0.558   9.604  11913  Z= 0.286
  Chirality :  0.041   0.213   1324
  Planarity :  0.004   0.070   1518
  Dihedral  :  4.004  43.050   1199
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.31 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 32.25 %
    Favored  : 63.52 %
  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:  0.63 (0.27), residues: 1054
  helix:  2.43 (0.26), residues: 416
  sheet: -1.01 (0.34), residues: 231
  loop : -0.81 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 283 
 TYR   0.025   0.001   TYR R 200 
 PHE   0.023   0.001   PHE P   6 
 TRP   0.015   0.001   TRP R 297 
 HIS   0.003   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 8795)
  covalent geometry    : angle       0.55814 (11909)
  SS BOND              : bond        0.00103 (    2)
  SS BOND              : angle       0.67782 (    4)
  hydrogen bonds       : bond        0.03517 (  423)
  hydrogen bonds       : angle       3.97380 ( 1194)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2614.19 seconds
wall clock time: 45 minutes 21.74 seconds (2721.74 seconds total)