Starting phenix.real_space_refine
on Tue Apr 29 03:20:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vhf_43236/04_2025/8vhf_43236.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vhf_43236/04_2025/8vhf_43236.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vhf_43236/04_2025/8vhf_43236.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vhf_43236/04_2025/8vhf_43236.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vhf_43236/04_2025/8vhf_43236.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vhf_43236/04_2025/8vhf_43236.cif"
  }
  resolution = 3.51
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.003 sd=   0.221
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    5258      2.51       5
     N    1455      2.21       5
     O    1530      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8299
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2606
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2606
          Classifications: {'peptide': 339}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "C"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "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: "A"
      Number of atoms: 1960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1960
          Classifications: {'peptide': 237}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 6, 'TRANS': 230}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "R"
      Number of atoms: 2289
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 296, 2289
          Classifications: {'peptide': 296}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 284}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "R"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'8VP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.71, per 1000 atoms: 0.69
  Number of scatterers: 8299
  At special positions: 0
  Unit cell: (73.6, 98.44, 130.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1530      8.00
     N    1455      7.00
     C    5258      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  78 " - pdb=" SG  CYS R 155 " 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: 2.14
  Conformation dependent library (CDL) restraints added in 984.1 milliseconds
  

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1978

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 10 sheets defined
      40.9% alpha, 18.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'B' and resid 13 through 37
    Processing helix  chain 'B' and resid 40 through 45
      removed outlier: 3.585A  pdb=" N   ILE B  44 " --> pdb=" O   THR B  40 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 8 through 23
    Processing helix  chain 'C' and resid 29 through 43
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.802A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 28 through 32'
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.726A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 4.330A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 58
    Processing helix  chain 'A' and resid 235 through 239
      removed outlier: 3.834A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 281 through 285
      removed outlier: 4.434A  pdb=" N   ASP A 284 " --> pdb=" O   TRP A 281 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR A 285 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 281 through 285'
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.974A  pdb=" N   ALA A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.810A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'R' and resid 6 through 37
      removed outlier: 3.809A  pdb=" N   ILE R  10 " --> pdb=" O   SER R   6 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   HIS R  34 " --> pdb=" O   LEU R  30 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   LYS R  35 " --> pdb=" O   LEU R  31 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 39 through 66
      removed outlier: 4.210A  pdb=" N   THR R  63 " --> pdb=" O   SER R  59 " (cutoff:3.500A)
      removed outlier: 5.567A  pdb=" N   ASP R  64 " --> pdb=" O   GLY R  60 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   GLN R  65 " --> pdb=" O   LEU R  61 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 74 through 109
      removed outlier: 3.570A  pdb=" N   CYS R  78 " --> pdb=" O   GLN R  74 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 109 through 114
    Processing helix  chain 'R' and resid 118 through 143
      Proline residue:  R 140  - end of helix
    Processing helix  chain 'R' and resid 163 through 173
      removed outlier: 3.566A  pdb=" N   LEU R 167 " --> pdb=" O   PRO R 163 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 174 through 209
      removed outlier: 3.629A  pdb=" N   ALA R 209 " --> pdb=" O   ALA R 205 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 221 through 249
      removed outlier: 4.020A  pdb=" N   TRP R 238 " --> pdb=" O   PHE R 234 " (cutoff:3.500A)
      Proline residue:  R 240  - end of helix
    Processing helix  chain 'R' and resid 256 through 263
    Processing helix  chain 'R' and resid 264 through 280
      removed outlier: 3.847A  pdb=" N   SER R 272 " --> pdb=" O   GLY R 268 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU R 273 " --> pdb=" O   VAL R 269 " (cutoff:3.500A)
      Proline residue:  R 276  - end of helix
    Processing helix  chain 'R' and resid 283 through 300
      removed outlier: 3.733A  pdb=" N   LYS R 299 " --> pdb=" O   LEU R 295 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   VAL R 300 " --> pdb=" O   GLY R 296 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.601A  pdb=" N   ILE B 349 " --> pdb=" O   ARG B  59 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   THR B  61 " --> pdb=" O   LEU B 347 " (cutoff:3.500A)
      removed outlier: 5.871A  pdb=" N   LEU B 347 " --> pdb=" O   THR B  61 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 69 through 73
      removed outlier: 3.793A  pdb=" N   ALA B  71 " --> pdb=" O   ALA B  84 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   HIS B  73 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   SER B  85 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 4.879A  pdb=" N   LYS B  89 " --> pdb=" O   SER B  85 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 111 through 116
      removed outlier: 3.561A  pdb=" N   GLY B 126 " --> pdb=" O   THR B 113 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 157 through 164
      removed outlier: 3.546A  pdb=" N   CYS B 159 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LEU B 163 " --> pdb=" O   GLN B 167 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   GLN B 167 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   ASP B 181 " --> pdb=" O   GLN B 187 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   GLN B 187 " --> pdb=" O   ASP B 181 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 200 through 203
      removed outlier: 3.674A  pdb=" N   SER B 200 " --> pdb=" O   GLY B 213 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   GLN B 231 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   ASP B 223 " --> pdb=" O   CYS B 229 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   CYS B 229 " --> pdb=" O   ASP B 223 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 240 through 245
      removed outlier: 3.782A  pdb=" N   MET B 273 " --> pdb=" O   LEU B 263 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   ASP B 265 " --> pdb=" O   GLU B 271 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   GLU B 271 " --> pdb=" O   ASP B 265 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 284 through 289
      removed outlier: 6.385A  pdb=" N   GLY B 299 " --> pdb=" O   THR B 285 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   VAL B 287 " --> pdb=" O   LEU B 297 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   LEU B 297 " --> pdb=" O   VAL B 287 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   PHE B 289 " --> pdb=" O   LEU B 295 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   LEU B 295 " --> pdb=" O   PHE B 289 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLY B 317 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   ASP B 309 " --> pdb=" O   ARG B 315 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   ARG B 315 " --> pdb=" O   ASP B 309 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 8
      removed outlier: 3.697A  pdb=" N   SER N  21 " --> pdb=" O   SER N   7 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 58 through 60
      removed outlier: 6.684A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ASN N  35 " --> pdb=" O   ALA N  97 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 207 through 213
      removed outlier: 4.223A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 9.407A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.711A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.257A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 5.521A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.749A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 8.142A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)

    413 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: 2.33

  Time building geometry restraints manager: 2.45 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2718
        1.34 -     1.46: 1853
        1.46 -     1.58: 3817
        1.58 -     1.70: 0
        1.70 -     1.82: 81
  Bond restraints: 8469
  Sorted by residual:
  bond pdb=" C14 8VP R 601 "
       pdb=" C19 8VP R 601 "
    ideal  model  delta    sigma   weight residual
    1.557  1.450  0.107 2.00e-02 2.50e+03 2.84e+01
  bond pdb=" C3  8VP R 601 "
       pdb=" N28 8VP R 601 "
    ideal  model  delta    sigma   weight residual
    1.423  1.324  0.099 2.00e-02 2.50e+03 2.47e+01
  bond pdb=" C20 8VP R 601 "
       pdb=" N17 8VP R 601 "
    ideal  model  delta    sigma   weight residual
    1.357  1.448 -0.091 2.00e-02 2.50e+03 2.08e+01
  bond pdb=" C14 8VP R 601 "
       pdb=" C15 8VP R 601 "
    ideal  model  delta    sigma   weight residual
    1.533  1.454  0.079 2.00e-02 2.50e+03 1.58e+01
  bond pdb=" N31 8VP R 601 "
       pdb=" N32 8VP R 601 "
    ideal  model  delta    sigma   weight residual
    1.288  1.364 -0.076 2.00e-02 2.50e+03 1.46e+01
  ... (remaining 8464 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.30: 11343
        3.30 -     6.59: 100
        6.59 -     9.89: 17
        9.89 -    13.19: 3
       13.19 -    16.49: 2
  Bond angle restraints: 11465
  Sorted by residual:
  angle pdb=" CA  LEU R 139 "
        pdb=" CB  LEU R 139 "
        pdb=" CG  LEU R 139 "
      ideal   model   delta    sigma   weight residual
     116.30  132.79  -16.49 3.50e+00 8.16e-02 2.22e+01
  angle pdb=" CA  LEU C  19 "
        pdb=" CB  LEU C  19 "
        pdb=" CG  LEU C  19 "
      ideal   model   delta    sigma   weight residual
     116.30  131.86  -15.56 3.50e+00 8.16e-02 1.98e+01
  angle pdb=" CA  ARG A  13 "
        pdb=" CB  ARG A  13 "
        pdb=" CG  ARG A  13 "
      ideal   model   delta    sigma   weight residual
     114.10  122.40   -8.30 2.00e+00 2.50e-01 1.72e+01
  angle pdb=" CA  LYS A 307 "
        pdb=" CB  LYS A 307 "
        pdb=" CG  LYS A 307 "
      ideal   model   delta    sigma   weight residual
     114.10  122.27   -8.17 2.00e+00 2.50e-01 1.67e+01
  angle pdb=" CA  GLU C  17 "
        pdb=" CB  GLU C  17 "
        pdb=" CG  GLU C  17 "
      ideal   model   delta    sigma   weight residual
     114.10  122.15   -8.05 2.00e+00 2.50e-01 1.62e+01
  ... (remaining 11460 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.99: 4545
       23.99 -    47.98: 455
       47.98 -    71.97: 47
       71.97 -    95.97: 15
       95.97 -   119.96: 1
  Dihedral angle restraints: 5063
    sinusoidal: 2000
      harmonic: 3063
  Sorted by residual:
  dihedral pdb=" CB  CYS R  78 "
           pdb=" SG  CYS R  78 "
           pdb=" SG  CYS R 155 "
           pdb=" CB  CYS R 155 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  176.08  -83.08     1      1.00e+01 1.00e-02 8.44e+01
  dihedral pdb=" C16 8VP R 601 "
           pdb=" C18 8VP R 601 "
           pdb=" N17 8VP R 601 "
           pdb=" C19 8VP R 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.31   59.65 -119.96     1      3.00e+01 1.11e-03 1.60e+01
  dihedral pdb=" CA  ASP R 220 "
           pdb=" C   ASP R 220 "
           pdb=" N   PHE R 221 "
           pdb=" CA  PHE R 221 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.10   17.90     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 5060 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 968
       0.045 -    0.091: 235
       0.091 -    0.136: 83
       0.136 -    0.181: 3
       0.181 -    0.226: 1
  Chirality restraints: 1290
  Sorted by residual:
  chirality pdb=" CB  ILE R 116 "
            pdb=" CA  ILE R 116 "
            pdb=" CG1 ILE R 116 "
            pdb=" CG2 ILE R 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.87   -0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CG  LEU R  77 "
            pdb=" CB  LEU R  77 "
            pdb=" CD1 LEU R  77 "
            pdb=" CD2 LEU R  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.25e-01
  chirality pdb=" CA  ASP R  51 "
            pdb=" N   ASP R  51 "
            pdb=" C   ASP R  51 "
            pdb=" CB  ASP R  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.40e-01
  ... (remaining 1287 not shown)

  Planarity restraints: 1463
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 215 "   -0.011 2.00e-02 2.50e+03   2.27e-02 5.15e+00
        pdb=" CG  ASP A 215 "    0.039 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 215 "   -0.014 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 215 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  20 "   -0.165 9.50e-02 1.11e+02   7.42e-02 3.72e+00
        pdb=" NE  ARG A  20 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  20 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  20 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  20 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 215 "    0.009 2.00e-02 2.50e+03   1.89e-02 3.56e+00
        pdb=" C   ASP A 215 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   ASP A 215 "    0.013 2.00e-02 2.50e+03
        pdb=" N   LYS A 216 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1460 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1538
        2.77 -     3.30: 7924
        3.30 -     3.83: 14325
        3.83 -     4.37: 15974
        4.37 -     4.90: 27864
  Nonbonded interactions: 67625
  Sorted by model distance:
  nonbonded pdb=" O   SER B  78 "
            pdb=" OG  SER B  78 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OH  TYR A 253 "
            pdb=" O   SER A 306 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   LYS R  75 "
            pdb=" OG  SER R  79 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   TRP N  47 "
            pdb=" OG1 THR N  61 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" O   SER R 233 "
            pdb=" OG  SER R 237 "
     model   vdw
     2.306 3.040
  ... (remaining 67620 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.550
  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:             0.020
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     22.700
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
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   0.107   8471  Z= 0.207
  Angle     :  0.823  16.485  11469  Z= 0.409
  Chirality :  0.044   0.226   1290
  Planarity :  0.004   0.074   1463
  Dihedral  : 17.720 119.958   3079
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  : 29.71 %
    Favored  : 69.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.25), residues: 1043
  helix:  1.15 (0.26), residues: 396
  sheet: -0.31 (0.34), residues: 195
  loop : -1.22 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 180 
 HIS   0.010   0.001   HIS R 292 
 PHE   0.031   0.001   PHE A 340 
 TYR   0.012   0.001   TYR B 275 
 ARG   0.010   0.000   ARG A  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10288 (  413)
  hydrogen bonds       : angle       5.99856 ( 1194)
  SS BOND              : bond        0.00181 (    2)
  SS BOND              : angle       1.03277 (    4)
  covalent geometry    : bond        0.00445 ( 8469)
  covalent geometry    : angle       0.82266 (11465)

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 187
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   18 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8552 (tp40)
REVERT: N   13 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8274 (mm-40)
REVERT: A   27 GLU cc_start: 0.8718 (tp30) cc_final: 0.8486 (tp30)
  outliers start: 3
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1997
  time to fit residues: 51.3094
Evaluate side-chains
  177 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.6980
   chunk 77 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 30 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.130031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.104875 restraints weight = 13377.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.108957 restraints weight = 7252.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.111723 restraints weight = 4890.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.0905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8471  Z= 0.135
  Angle     :  0.586  11.382  11469  Z= 0.295
  Chirality :  0.041   0.139   1290
  Planarity :  0.004   0.039   1463
  Dihedral  :  5.623  54.201   1178
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 28.14 %
    Favored  : 68.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.26), residues: 1043
  helix:  1.56 (0.26), residues: 404
  sheet: -0.29 (0.33), residues: 217
  loop : -1.02 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 222 
 HIS   0.006   0.001   HIS B 236 
 PHE   0.012   0.001   PHE A 340 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.007   0.000   ARG C  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03730 (  413)
  hydrogen bonds       : angle       4.82929 ( 1194)
  SS BOND              : bond        0.00133 (    2)
  SS BOND              : angle       0.64616 (    4)
  covalent geometry    : bond        0.00308 ( 8469)
  covalent geometry    : angle       0.58587 (11465)

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 194
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   70 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.7802 (m-80)
REVERT: B  300 TYR cc_start: 0.8346 (m-80) cc_final: 0.8107 (m-80)
REVERT: C   18 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8349 (tp40)
REVERT: C   27 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7144 (mmm-85)
REVERT: N   13 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8423 (mm-40)
REVERT: N   90 ASP cc_start: 0.8780 (t0) cc_final: 0.8478 (t0)
REVERT: A   27 GLU cc_start: 0.8660 (tp30) cc_final: 0.8424 (tp30)
REVERT: A  253 TYR cc_start: 0.5208 (p90) cc_final: 0.4901 (p90)
REVERT: A  390 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7882 (tm-30)
REVERT: R  145 MET cc_start: 0.7803 (tpp) cc_final: 0.7405 (tpp)
  outliers start: 28
  outliers final: 17
  residues processed: 209
  average time/residue: 0.1897
  time to fit residues: 55.3172
Evaluate side-chains
  192 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 173
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  236 HIS
Chi-restraints excluded: chain B residue  277 HIS
Chi-restraints excluded: chain C residue   27 ARG
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain R residue   19 ILE
Chi-restraints excluded: chain R residue   56 VAL
Chi-restraints excluded: chain R residue   97 MET
Chi-restraints excluded: chain R residue  102 ASP
Chi-restraints excluded: chain R residue  266 LEU
Chi-restraints excluded: chain R residue  272 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 30 optimal weight:    8.9990
   chunk 47 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0000
   chunk 19 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 82 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9990
   chunk 34 optimal weight:    7.9990
   chunk 69 optimal weight:    7.9990
   chunk 85 optimal weight:    0.7980
   overall best weight:    1.5590

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

Flipped N/Q/H residues before XYZ refinement:
B  43 GLN
A 220 HIS
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 292 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.124136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.098565 restraints weight = 13732.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.102527 restraints weight = 7454.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.105185 restraints weight = 5074.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.1522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8471  Z= 0.215
  Angle     :  0.619   8.751  11469  Z= 0.320
  Chirality :  0.043   0.149   1290
  Planarity :  0.004   0.040   1463
  Dihedral  :  5.847  50.124   1178
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 29.04 %
    Favored  : 66.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.26), residues: 1043
  helix:  1.58 (0.26), residues: 399
  sheet: -0.43 (0.33), residues: 224
  loop : -1.06 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 222 
 HIS   0.009   0.001   HIS B 236 
 PHE   0.020   0.002   PHE A 340 
 TYR   0.020   0.002   TYR A 391 
 ARG   0.003   0.000   ARG N  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04029 (  413)
  hydrogen bonds       : angle       4.88350 ( 1194)
  SS BOND              : bond        0.00083 (    2)
  SS BOND              : angle       0.85167 (    4)
  covalent geometry    : bond        0.00493 ( 8469)
  covalent geometry    : angle       0.61927 (11465)

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 181
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   70 TYR cc_start: 0.8919 (OUTLIER) cc_final: 0.8098 (m-80)
REVERT: C   27 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.7323 (mmm-85)
REVERT: N   13 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8475 (mm-40)
REVERT: N   73 ASP cc_start: 0.7406 (t0) cc_final: 0.6871 (t70)
REVERT: N   90 ASP cc_start: 0.8974 (t0) cc_final: 0.8734 (t0)
REVERT: A   19 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8321 (tt0)
REVERT: A   27 GLU cc_start: 0.8716 (tp30) cc_final: 0.8433 (tp30)
REVERT: A  339 TYR cc_start: 0.8265 (m-80) cc_final: 0.7897 (m-80)
REVERT: A  390 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7905 (tm-30)
REVERT: R  145 MET cc_start: 0.7856 (tpp) cc_final: 0.7444 (tpp)
REVERT: R  258 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7928 (pp)
  outliers start: 42
  outliers final: 28
  residues processed: 208
  average time/residue: 0.1898
  time to fit residues: 54.9577
Evaluate side-chains
  201 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 169
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 LYS
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   43 GLN
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  236 HIS
Chi-restraints excluded: chain B residue  277 HIS
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   27 ARG
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain A residue   19 GLN
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain R residue   19 ILE
Chi-restraints excluded: chain R residue   23 THR
Chi-restraints excluded: chain R residue   97 MET
Chi-restraints excluded: chain R residue  102 ASP
Chi-restraints excluded: chain R residue  155 CYS
Chi-restraints excluded: chain R residue  169 LEU
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  258 LEU
Chi-restraints excluded: chain R residue  266 LEU
Chi-restraints excluded: chain R residue  272 SER
Chi-restraints excluded: chain R residue  292 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 87 optimal weight:    0.7980
   chunk 89 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0770
   chunk 20 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 78 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 292 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.127287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.102410 restraints weight = 13398.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.106468 restraints weight = 7113.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.109189 restraints weight = 4757.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.1525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8471  Z= 0.133
  Angle     :  0.591  11.136  11469  Z= 0.297
  Chirality :  0.041   0.137   1290
  Planarity :  0.003   0.038   1463
  Dihedral  :  5.548  47.307   1178
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 28.14 %
    Favored  : 66.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.26), residues: 1043
  helix:  1.68 (0.26), residues: 402
  sheet: -0.39 (0.32), residues: 223
  loop : -0.96 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 180 
 HIS   0.010   0.001   HIS R 292 
 PHE   0.019   0.001   PHE A 340 
 TYR   0.020   0.001   TYR A 391 
 ARG   0.002   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03668 (  413)
  hydrogen bonds       : angle       4.71674 ( 1194)
  SS BOND              : bond        0.00350 (    2)
  SS BOND              : angle       1.18918 (    4)
  covalent geometry    : bond        0.00304 ( 8469)
  covalent geometry    : angle       0.59056 (11465)

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 186
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   26 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8614 (tmtt)
REVERT: B   70 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.7830 (m-80)
REVERT: C   18 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8398 (tp40)
REVERT: C   27 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.7246 (mmm-85)
REVERT: N   13 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8469 (mm-40)
REVERT: N   73 ASP cc_start: 0.7437 (t0) cc_final: 0.6995 (t0)
REVERT: N   90 ASP cc_start: 0.8953 (t0) cc_final: 0.8704 (t0)
REVERT: A   27 GLU cc_start: 0.8696 (tp30) cc_final: 0.8413 (tp30)
REVERT: A  253 TYR cc_start: 0.5567 (p90) cc_final: 0.5324 (p90)
REVERT: R  145 MET cc_start: 0.7804 (tpp) cc_final: 0.7418 (tpp)
  outliers start: 47
  outliers final: 32
  residues processed: 212
  average time/residue: 0.1901
  time to fit residues: 55.7585
Evaluate side-chains
  212 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 177
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 LYS
Chi-restraints excluded: chain B residue   54 ILE
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  236 HIS
Chi-restraints excluded: chain B residue  277 HIS
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   27 ARG
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  112 SER
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain R residue   14 LEU
Chi-restraints excluded: chain R residue   19 ILE
Chi-restraints excluded: chain R residue   39 VAL
Chi-restraints excluded: chain R residue   56 VAL
Chi-restraints excluded: chain R residue   97 MET
Chi-restraints excluded: chain R residue  102 ASP
Chi-restraints excluded: chain R residue  155 CYS
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain R residue  266 LEU
Chi-restraints excluded: chain R residue  272 SER
Chi-restraints excluded: chain R residue  292 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0870
   chunk 33 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.1562

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

Flipped N/Q/H residues before XYZ refinement:
B  99 ASN
B 306 ASN
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 292 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.125199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.100120 restraints weight = 13496.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.104049 restraints weight = 7335.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.106746 restraints weight = 4983.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8471  Z= 0.173
  Angle     :  0.614   9.170  11469  Z= 0.312
  Chirality :  0.042   0.156   1290
  Planarity :  0.003   0.039   1463
  Dihedral  :  5.607  47.943   1178
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  5.61 %
    Allowed  : 28.70 %
    Favored  : 65.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.26), residues: 1043
  helix:  1.72 (0.26), residues: 392
  sheet: -0.41 (0.32), residues: 223
  loop : -0.94 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 222 
 HIS   0.009   0.001   HIS R 292 
 PHE   0.020   0.001   PHE A 340 
 TYR   0.017   0.002   TYR A 391 
 ARG   0.002   0.000   ARG N  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03765 (  413)
  hydrogen bonds       : angle       4.76086 ( 1194)
  SS BOND              : bond        0.00133 (    2)
  SS BOND              : angle       1.18348 (    4)
  covalent geometry    : bond        0.00400 ( 8469)
  covalent geometry    : angle       0.61330 (11465)

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 185
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   26 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8846 (mtpp)
REVERT: B   70 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.7937 (m-80)
REVERT: C   18 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8188 (tp40)
REVERT: C   20 LYS cc_start: 0.9153 (mtpp) cc_final: 0.8944 (mtpp)
REVERT: C   21 MET cc_start: 0.8278 (tmm) cc_final: 0.7690 (tmm)
REVERT: C   22 GLU cc_start: 0.8508 (pp20) cc_final: 0.8268 (pp20)
REVERT: C   27 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7301 (mmm-85)
REVERT: N   13 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8487 (mm-40)
REVERT: N   73 ASP cc_start: 0.7482 (t0) cc_final: 0.7048 (t0)
REVERT: N   90 ASP cc_start: 0.8912 (t0) cc_final: 0.8701 (t0)
REVERT: A   27 GLU cc_start: 0.8695 (tp30) cc_final: 0.8417 (tp30)
REVERT: A  378 ASP cc_start: 0.8178 (m-30) cc_final: 0.7855 (t0)
REVERT: R  258 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7963 (pp)
REVERT: R  260 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8689 (mp)
REVERT: R  284 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8511 (mmmt)
  outliers start: 50
  outliers final: 38
  residues processed: 215
  average time/residue: 0.1933
  time to fit residues: 57.4736
Evaluate side-chains
  220 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 177
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 LYS
Chi-restraints excluded: chain B residue   54 ILE
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  236 HIS
Chi-restraints excluded: chain B residue  277 HIS
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   27 ARG
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   74 ASN
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  112 SER
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain R residue   14 LEU
Chi-restraints excluded: chain R residue   19 ILE
Chi-restraints excluded: chain R residue   39 VAL
Chi-restraints excluded: chain R residue   51 ASP
Chi-restraints excluded: chain R residue   56 VAL
Chi-restraints excluded: chain R residue   97 MET
Chi-restraints excluded: chain R residue  102 ASP
Chi-restraints excluded: chain R residue  155 CYS
Chi-restraints excluded: chain R residue  169 LEU
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain R residue  258 LEU
Chi-restraints excluded: chain R residue  260 LEU
Chi-restraints excluded: chain R residue  266 LEU
Chi-restraints excluded: chain R residue  272 SER
Chi-restraints excluded: chain R residue  292 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 78 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 99 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 292 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.124873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.099697 restraints weight = 13557.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.103697 restraints weight = 7190.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.106423 restraints weight = 4820.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8471  Z= 0.169
  Angle     :  0.612  11.568  11469  Z= 0.311
  Chirality :  0.042   0.152   1290
  Planarity :  0.003   0.039   1463
  Dihedral  :  5.592  47.483   1178
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  6.39 %
    Allowed  : 28.14 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.26), residues: 1043
  helix:  1.74 (0.26), residues: 392
  sheet: -0.50 (0.32), residues: 228
  loop : -0.88 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 180 
 HIS   0.010   0.001   HIS R 292 
 PHE   0.020   0.001   PHE A 340 
 TYR   0.023   0.001   TYR A 391 
 ARG   0.003   0.000   ARG C  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03748 (  413)
  hydrogen bonds       : angle       4.73305 ( 1194)
  SS BOND              : bond        0.00087 (    2)
  SS BOND              : angle       1.01025 (    4)
  covalent geometry    : bond        0.00391 ( 8469)
  covalent geometry    : angle       0.61214 (11465)

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 186
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   26 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8873 (mtpp)
REVERT: B   70 TYR cc_start: 0.8889 (OUTLIER) cc_final: 0.7848 (m-80)
REVERT: C   27 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.7262 (mmm-85)
REVERT: N   13 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8474 (mm-40)
REVERT: N   38 ARG cc_start: 0.8882 (ptt180) cc_final: 0.8616 (ptt180)
REVERT: N   73 ASP cc_start: 0.7584 (t0) cc_final: 0.7104 (t0)
REVERT: N  108 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7670 (m-80)
REVERT: A   27 GLU cc_start: 0.8710 (tp30) cc_final: 0.8416 (tp30)
REVERT: A  253 TYR cc_start: 0.5516 (p90) cc_final: 0.5290 (p90)
REVERT: A  378 ASP cc_start: 0.8174 (m-30) cc_final: 0.7860 (t0)
REVERT: A  390 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7958 (tm-30)
REVERT: R  258 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.8003 (pp)
REVERT: R  260 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8703 (mp)
REVERT: R  284 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8626 (mmmt)
  outliers start: 57
  outliers final: 41
  residues processed: 219
  average time/residue: 0.1954
  time to fit residues: 59.6944
Evaluate side-chains
  227 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 180
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 LYS
Chi-restraints excluded: chain B residue   54 ILE
Chi-restraints excluded: chain B residue   68 LYS
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  236 HIS
Chi-restraints excluded: chain B residue  277 HIS
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   27 ARG
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   74 ASN
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  112 SER
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain R residue   14 LEU
Chi-restraints excluded: chain R residue   19 ILE
Chi-restraints excluded: chain R residue   23 THR
Chi-restraints excluded: chain R residue   39 VAL
Chi-restraints excluded: chain R residue   56 VAL
Chi-restraints excluded: chain R residue   97 MET
Chi-restraints excluded: chain R residue  102 ASP
Chi-restraints excluded: chain R residue  155 CYS
Chi-restraints excluded: chain R residue  169 LEU
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  258 LEU
Chi-restraints excluded: chain R residue  260 LEU
Chi-restraints excluded: chain R residue  266 LEU
Chi-restraints excluded: chain R residue  272 SER
Chi-restraints excluded: chain R residue  292 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 91 optimal weight:    0.7980
   chunk 43 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9980
   chunk 16 optimal weight:    0.2980
   chunk 48 optimal weight:    0.3980
   chunk 61 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 86 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 76 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 292 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.127232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.102395 restraints weight = 13520.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.106374 restraints weight = 7241.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.109082 restraints weight = 4887.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8471  Z= 0.131
  Angle     :  0.613  12.507  11469  Z= 0.309
  Chirality :  0.042   0.149   1290
  Planarity :  0.003   0.039   1463
  Dihedral  :  5.421  44.197   1178
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 29.48 %
    Favored  : 65.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.26), residues: 1043
  helix:  1.83 (0.26), residues: 389
  sheet: -0.35 (0.33), residues: 223
  loop : -0.88 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 180 
 HIS   0.008   0.001   HIS B 236 
 PHE   0.019   0.001   PHE A 340 
 TYR   0.020   0.001   TYR A 391 
 ARG   0.003   0.000   ARG C  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03602 (  413)
  hydrogen bonds       : angle       4.66752 ( 1194)
  SS BOND              : bond        0.00059 (    2)
  SS BOND              : angle       0.77331 (    4)
  covalent geometry    : bond        0.00302 ( 8469)
  covalent geometry    : angle       0.61300 (11465)

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 194
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   26 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8870 (mtpp)
REVERT: B   70 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.7689 (m-80)
REVERT: C   18 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8313 (tp40)
REVERT: C   27 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.7086 (mmm-85)
REVERT: N    1 GLN cc_start: 0.7709 (pm20) cc_final: 0.7501 (pm20)
REVERT: N   13 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8477 (mm-40)
REVERT: N   73 ASP cc_start: 0.7519 (t0) cc_final: 0.7076 (t0)
REVERT: A   13 ARG cc_start: 0.7783 (mpt180) cc_final: 0.7328 (mpt180)
REVERT: A  262 GLN cc_start: 0.7867 (mp10) cc_final: 0.7637 (mp10)
REVERT: A  390 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7893 (tm-30)
REVERT: R   35 LYS cc_start: 0.8544 (ttpp) cc_final: 0.8328 (mtpt)
REVERT: R  258 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8028 (pp)
REVERT: R  284 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8616 (mmmt)
  outliers start: 47
  outliers final: 33
  residues processed: 219
  average time/residue: 0.1991
  time to fit residues: 60.2851
Evaluate side-chains
  219 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 182
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 LYS
Chi-restraints excluded: chain B residue   54 ILE
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  236 HIS
Chi-restraints excluded: chain B residue  277 HIS
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  350 TRP
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   27 ARG
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   74 ASN
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  112 SER
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain R residue   14 LEU
Chi-restraints excluded: chain R residue   19 ILE
Chi-restraints excluded: chain R residue   39 VAL
Chi-restraints excluded: chain R residue   51 ASP
Chi-restraints excluded: chain R residue   56 VAL
Chi-restraints excluded: chain R residue   97 MET
Chi-restraints excluded: chain R residue  102 ASP
Chi-restraints excluded: chain R residue  155 CYS
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain R residue  258 LEU
Chi-restraints excluded: chain R residue  266 LEU
Chi-restraints excluded: chain R residue  272 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 96 optimal weight:    0.0470
   chunk 37 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   overall best weight:    1.1882

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 292 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.124767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.099620 restraints weight = 13774.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.103538 restraints weight = 7431.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.106154 restraints weight = 5028.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8471  Z= 0.180
  Angle     :  0.646  12.150  11469  Z= 0.327
  Chirality :  0.043   0.147   1290
  Planarity :  0.004   0.039   1463
  Dihedral  :  5.588  44.986   1178
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  5.72 %
    Allowed  : 29.60 %
    Favored  : 64.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.26), residues: 1043
  helix:  1.70 (0.26), residues: 392
  sheet: -0.62 (0.32), residues: 232
  loop : -0.83 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 222 
 HIS   0.010   0.001   HIS R 292 
 PHE   0.020   0.002   PHE A 340 
 TYR   0.023   0.002   TYR A 391 
 ARG   0.003   0.000   ARG C  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03803 (  413)
  hydrogen bonds       : angle       4.72858 ( 1194)
  SS BOND              : bond        0.00117 (    2)
  SS BOND              : angle       0.99928 (    4)
  covalent geometry    : bond        0.00418 ( 8469)
  covalent geometry    : angle       0.64586 (11465)

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 185
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   26 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8873 (mtpp)
REVERT: B   70 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.7763 (m-80)
REVERT: B  226 GLU cc_start: 0.8198 (pm20) cc_final: 0.7857 (pm20)
REVERT: B  306 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8273 (p0)
REVERT: C   18 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8382 (tp40)
REVERT: C   27 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.7127 (mmm-85)
REVERT: N    1 GLN cc_start: 0.7771 (pm20) cc_final: 0.7562 (pm20)
REVERT: N   73 ASP cc_start: 0.7566 (t0) cc_final: 0.7124 (t0)
REVERT: N  108 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7715 (m-80)
REVERT: A   13 ARG cc_start: 0.7829 (mpt180) cc_final: 0.7231 (mpt180)
REVERT: R  258 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8086 (pp)
REVERT: R  284 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8478 (mmpt)
  outliers start: 51
  outliers final: 39
  residues processed: 214
  average time/residue: 0.1964
  time to fit residues: 58.1835
Evaluate side-chains
  222 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 177
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 LYS
Chi-restraints excluded: chain B residue   54 ILE
Chi-restraints excluded: chain B residue   68 LYS
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  236 HIS
Chi-restraints excluded: chain B residue  277 HIS
Chi-restraints excluded: chain B residue  306 ASN
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  350 TRP
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   27 ARG
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   74 ASN
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  112 SER
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain R residue   14 LEU
Chi-restraints excluded: chain R residue   19 ILE
Chi-restraints excluded: chain R residue   23 THR
Chi-restraints excluded: chain R residue   39 VAL
Chi-restraints excluded: chain R residue   51 ASP
Chi-restraints excluded: chain R residue   56 VAL
Chi-restraints excluded: chain R residue   97 MET
Chi-restraints excluded: chain R residue  102 ASP
Chi-restraints excluded: chain R residue  155 CYS
Chi-restraints excluded: chain R residue  258 LEU
Chi-restraints excluded: chain R residue  266 LEU
Chi-restraints excluded: chain R residue  272 SER
Chi-restraints excluded: chain R residue  292 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0170
   chunk 0 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.8224

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 292 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.126923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.101738 restraints weight = 13848.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.105865 restraints weight = 7221.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.108617 restraints weight = 4785.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8471  Z= 0.150
  Angle     :  0.650  13.531  11469  Z= 0.326
  Chirality :  0.042   0.140   1290
  Planarity :  0.003   0.039   1463
  Dihedral  :  5.495  43.480   1178
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 30.38 %
    Favored  : 64.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.26), residues: 1043
  helix:  1.70 (0.26), residues: 392
  sheet: -0.54 (0.32), residues: 227
  loop : -0.83 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 180 
 HIS   0.013   0.001   HIS R 292 
 PHE   0.017   0.001   PHE A 340 
 TYR   0.023   0.002   TYR A 391 
 ARG   0.003   0.000   ARG C  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03684 (  413)
  hydrogen bonds       : angle       4.68206 ( 1194)
  SS BOND              : bond        0.00089 (    2)
  SS BOND              : angle       0.83580 (    4)
  covalent geometry    : bond        0.00349 ( 8469)
  covalent geometry    : angle       0.65009 (11465)

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 182
  time to evaluate  : 1.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   26 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8865 (mtpp)
REVERT: B   70 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.7660 (m-80)
REVERT: B  306 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8180 (p0)
REVERT: C   18 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8279 (tp40)
REVERT: C   27 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7040 (mmm-85)
REVERT: N   73 ASP cc_start: 0.7613 (t0) cc_final: 0.7155 (t0)
REVERT: A   13 ARG cc_start: 0.7837 (mpt180) cc_final: 0.7001 (mpt180)
REVERT: A   60 MET cc_start: 0.6654 (pmm) cc_final: 0.6405 (pmm)
REVERT: A  390 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7908 (tm-30)
REVERT: R   35 LYS cc_start: 0.8583 (ttpp) cc_final: 0.8330 (mtpt)
REVERT: R  258 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8115 (pp)
REVERT: R  284 LYS cc_start: 0.8755 (mmmt) cc_final: 0.8474 (mmpt)
  outliers start: 48
  outliers final: 40
  residues processed: 207
  average time/residue: 0.2493
  time to fit residues: 72.7159
Evaluate side-chains
  225 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 180
  time to evaluate  : 1.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 LYS
Chi-restraints excluded: chain B residue   54 ILE
Chi-restraints excluded: chain B residue   68 LYS
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  236 HIS
Chi-restraints excluded: chain B residue  277 HIS
Chi-restraints excluded: chain B residue  306 ASN
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  350 TRP
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   27 ARG
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   74 ASN
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  112 SER
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain R residue   14 LEU
Chi-restraints excluded: chain R residue   19 ILE
Chi-restraints excluded: chain R residue   39 VAL
Chi-restraints excluded: chain R residue   51 ASP
Chi-restraints excluded: chain R residue   56 VAL
Chi-restraints excluded: chain R residue   97 MET
Chi-restraints excluded: chain R residue  102 ASP
Chi-restraints excluded: chain R residue  155 CYS
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  258 LEU
Chi-restraints excluded: chain R residue  266 LEU
Chi-restraints excluded: chain R residue  272 SER
Chi-restraints excluded: chain R residue  292 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 69 optimal weight:    8.9990
   chunk 84 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 87 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
N  13 GLN
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 292 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.125618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.100788 restraints weight = 13722.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.104703 restraints weight = 7342.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.107345 restraints weight = 4950.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.2052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8471  Z= 0.178
  Angle     :  0.680  13.483  11469  Z= 0.342
  Chirality :  0.043   0.186   1290
  Planarity :  0.004   0.040   1463
  Dihedral  :  5.589  44.311   1178
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 30.49 %
    Favored  : 64.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.26), residues: 1043
  helix:  1.63 (0.26), residues: 392
  sheet: -0.54 (0.33), residues: 227
  loop : -0.84 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 222 
 HIS   0.017   0.001   HIS R 292 
 PHE   0.029   0.002   PHE A 340 
 TYR   0.030   0.002   TYR A 391 
 ARG   0.003   0.000   ARG C  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03773 (  413)
  hydrogen bonds       : angle       4.74187 ( 1194)
  SS BOND              : bond        0.00100 (    2)
  SS BOND              : angle       0.95030 (    4)
  covalent geometry    : bond        0.00415 ( 8469)
  covalent geometry    : angle       0.67999 (11465)

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 182
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   26 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8864 (mtpp)
REVERT: B   70 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.7747 (m-80)
REVERT: B  306 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8481 (p0)
REVERT: C   18 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8350 (tp40)
REVERT: C   27 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.7098 (mmm-85)
REVERT: N   13 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8386 (mm-40)
REVERT: N   73 ASP cc_start: 0.7586 (t0) cc_final: 0.7151 (t0)
REVERT: A   13 ARG cc_start: 0.7722 (mpt180) cc_final: 0.7124 (mpt180)
REVERT: A  253 TYR cc_start: 0.5470 (p90) cc_final: 0.4997 (p90)
REVERT: A  390 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7916 (tm-30)
REVERT: R  284 LYS cc_start: 0.8728 (mmmt) cc_final: 0.8456 (mmpt)
  outliers start: 48
  outliers final: 39
  residues processed: 206
  average time/residue: 0.1908
  time to fit residues: 54.6684
Evaluate side-chains
  221 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 178
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 LYS
Chi-restraints excluded: chain B residue   54 ILE
Chi-restraints excluded: chain B residue   68 LYS
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  236 HIS
Chi-restraints excluded: chain B residue  277 HIS
Chi-restraints excluded: chain B residue  306 ASN
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  350 TRP
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   27 ARG
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue   74 ASN
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  112 SER
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain R residue   14 LEU
Chi-restraints excluded: chain R residue   19 ILE
Chi-restraints excluded: chain R residue   39 VAL
Chi-restraints excluded: chain R residue   51 ASP
Chi-restraints excluded: chain R residue   56 VAL
Chi-restraints excluded: chain R residue   97 MET
Chi-restraints excluded: chain R residue  155 CYS
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  266 LEU
Chi-restraints excluded: chain R residue  272 SER
Chi-restraints excluded: chain R residue  292 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9990
   chunk 27 optimal weight:    0.1980
   chunk 70 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 82 optimal weight:    0.7980
   chunk 90 optimal weight:    0.7980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 292 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.127719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.102850 restraints weight = 13649.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.106925 restraints weight = 7160.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.109625 restraints weight = 4755.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8471  Z= 0.142
  Angle     :  0.677  13.885  11469  Z= 0.337
  Chirality :  0.042   0.156   1290
  Planarity :  0.003   0.040   1463
  Dihedral  :  5.475  42.616   1178
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 31.39 %
    Favored  : 64.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.26), residues: 1043
  helix:  1.69 (0.26), residues: 392
  sheet: -0.51 (0.32), residues: 232
  loop : -0.81 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 180 
 HIS   0.013   0.001   HIS R 292 
 PHE   0.022   0.001   PHE R 101 
 TYR   0.032   0.002   TYR A 391 
 ARG   0.003   0.000   ARG C  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03638 (  413)
  hydrogen bonds       : angle       4.67346 ( 1194)
  SS BOND              : bond        0.00079 (    2)
  SS BOND              : angle       0.79979 (    4)
  covalent geometry    : bond        0.00330 ( 8469)
  covalent geometry    : angle       0.67729 (11465)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3511.70 seconds
wall clock time: 63 minutes 50.26 seconds (3830.26 seconds total)