Starting phenix.real_space_refine
on Wed Mar 12 21:26:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vhf_43236/03_2025/8vhf_43236.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vhf_43236/03_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_43236/03_2025/8vhf_43236.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vhf_43236/03_2025/8vhf_43236.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vhf_43236/03_2025/8vhf_43236.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vhf_43236/03_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-5624/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: 7.18, per 1000 atoms: 0.87
  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: 2.05
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.81
  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: 2.29

  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:             2.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     24.120
  Find NCS groups from input model:        0.090
  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:             0.010
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.010
-------------------------------------------------------------------------------
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   8469  Z= 0.285
  Angle     :  0.823  16.485  11465  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 

*********************** 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  : 0.845 
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: 0.2005
  time to fit residues: 51.5064
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  : 0.808 
-------------------------------------------------------------------------------
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   8469  Z= 0.200
  Angle     :  0.586  11.382  11465  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 

*********************** 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  : 0.881 
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: 0.1884
  time to fit residues: 54.9098
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  : 0.912 
-------------------------------------------------------------------------------
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:    4.9990
   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   8469  Z= 0.326
  Angle     :  0.619   8.751  11465  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 

*********************** 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  : 0.940 
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: 0.1897
  time to fit residues: 54.6798
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  : 0.857 
-------------------------------------------------------------------------------
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:    2.9990
   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:    0.7140

-------------------------------------------------------------------------------
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 = 0.3636 r_free = 0.3636 target = 0.127103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.102080 restraints weight = 13414.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.106130 restraints weight = 7152.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.108921 restraints weight = 4792.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.1530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8469  Z= 0.201
  Angle     :  0.592  11.196  11465  Z= 0.298
  Chirality :  0.041   0.137   1290
  Planarity :  0.003   0.038   1463
  Dihedral  :  5.560  47.458   1178
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 28.25 %
    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:  0.25 (0.26), residues: 1043
  helix:  1.67 (0.26), residues: 402
  sheet: -0.40 (0.32), residues: 223
  loop : -0.97 (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 

*********************** 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
  232 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 186
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   26 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8612 (tmtt)
REVERT: B   70 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.7833 (m-80)
REVERT: C   18 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8390 (tp40)
REVERT: C   27 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.7248 (mmm-85)
REVERT: N   13 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8470 (mm-40)
REVERT: N   73 ASP cc_start: 0.7435 (t0) cc_final: 0.6992 (t0)
REVERT: N   90 ASP cc_start: 0.8956 (t0) cc_final: 0.8706 (t0)
REVERT: A   27 GLU cc_start: 0.8701 (tp30) cc_final: 0.8421 (tp30)
REVERT: A  253 TYR cc_start: 0.5568 (p90) cc_final: 0.5322 (p90)
REVERT: R  145 MET cc_start: 0.7806 (tpp) cc_final: 0.7416 (tpp)
  outliers start: 46
  outliers final: 31
  residues processed: 212
  average time/residue: 0.1803
  time to fit residues: 53.1840
Evaluate side-chains
  210 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 176
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
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 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:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.3988

-------------------------------------------------------------------------------
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 = 0.3597 r_free = 0.3597 target = 0.124056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.098890 restraints weight = 13555.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.102815 restraints weight = 7398.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.105448 restraints weight = 5027.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8469  Z= 0.302
  Angle     :  0.627   8.928  11465  Z= 0.320
  Chirality :  0.043   0.159   1290
  Planarity :  0.004   0.040   1463
  Dihedral  :  5.718  49.259   1178
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 28.25 %
    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:  0.20 (0.26), residues: 1043
  helix:  1.66 (0.26), residues: 392
  sheet: -0.53 (0.32), residues: 228
  loop : -0.90 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 222 
 HIS   0.016   0.001   HIS R 292 
 PHE   0.021   0.001   PHE A 340 
 TYR   0.018   0.002   TYR A 391 
 ARG   0.002   0.000   ARG N  98 

*********************** 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
  237 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 183
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   26 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8861 (mtpp)
REVERT: B   70 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.7968 (m-80)
REVERT: C   20 LYS cc_start: 0.9150 (mtpp) cc_final: 0.8946 (mtpp)
REVERT: C   27 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.7299 (mmm-85)
REVERT: N   13 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8483 (mm-40)
REVERT: N   73 ASP cc_start: 0.7508 (t0) cc_final: 0.7064 (t0)
REVERT: N   90 ASP cc_start: 0.8931 (t0) cc_final: 0.8719 (t0)
REVERT: N  108 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7716 (m-80)
REVERT: A   27 GLU cc_start: 0.8701 (tp30) cc_final: 0.8419 (tp30)
REVERT: A  378 ASP cc_start: 0.8143 (m-30) cc_final: 0.7827 (t0)
REVERT: R  258 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7992 (pp)
REVERT: R  260 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8715 (mp)
REVERT: R  284 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8517 (mmmt)
  outliers start: 54
  outliers final: 41
  residues processed: 215
  average time/residue: 0.1932
  time to fit residues: 57.5166
Evaluate side-chains
  222 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 175
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 LYS
Chi-restraints excluded: chain B residue   40 THR
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 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   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  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
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:    4.9990
   chunk 45 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   chunk 27 optimal weight:    0.1980
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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 = 0.3635 r_free = 0.3635 target = 0.127073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.102091 restraints weight = 13419.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.106145 restraints weight = 7131.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.108905 restraints weight = 4779.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8469  Z= 0.196
  Angle     :  0.601  11.483  11465  Z= 0.303
  Chirality :  0.041   0.143   1290
  Planarity :  0.003   0.038   1463
  Dihedral  :  5.430  44.758   1178
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 29.04 %
    Favored  : 65.13 %
  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:  0.34 (0.26), residues: 1043
  helix:  1.80 (0.26), residues: 392
  sheet: -0.44 (0.32), residues: 225
  loop : -0.87 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 180 
 HIS   0.008   0.001   HIS R 292 
 PHE   0.019   0.001   PHE A 340 
 TYR   0.019   0.001   TYR A 391 
 ARG   0.003   0.000   ARG C  13 

*********************** 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
  246 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 194
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   26 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8867 (mtpp)
REVERT: B   70 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.7749 (m-80)
REVERT: C   18 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8374 (tp40)
REVERT: C   27 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.7267 (mmm-85)
REVERT: N    1 GLN cc_start: 0.7697 (pm20) cc_final: 0.7454 (pm20)
REVERT: N   13 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8488 (mm-40)
REVERT: N   38 ARG cc_start: 0.8862 (ptt180) cc_final: 0.8616 (ptt180)
REVERT: N   73 ASP cc_start: 0.7506 (t0) cc_final: 0.7067 (t0)
REVERT: A   27 GLU cc_start: 0.8682 (tp30) cc_final: 0.8387 (tp30)
REVERT: A  253 TYR cc_start: 0.5528 (p90) cc_final: 0.5295 (p90)
REVERT: A  378 ASP cc_start: 0.8094 (m-30) cc_final: 0.7800 (t0)
REVERT: A  390 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7993 (tm-30)
REVERT: R   35 LYS cc_start: 0.8538 (ttpp) cc_final: 0.8323 (mtpt)
REVERT: R  258 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8024 (pp)
REVERT: R  284 LYS cc_start: 0.8890 (mmmt) cc_final: 0.8540 (mmmt)
  outliers start: 52
  outliers final: 38
  residues processed: 224
  average time/residue: 0.1957
  time to fit residues: 61.4124
Evaluate side-chains
  226 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 184
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
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 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   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   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  180 LEU
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
Chi-restraints excluded: chain R residue  288 LEU
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:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.127379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.102239 restraints weight = 13556.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.106320 restraints weight = 7301.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.109044 restraints weight = 4912.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8469  Z= 0.200
  Angle     :  0.619  12.322  11465  Z= 0.309
  Chirality :  0.041   0.144   1290
  Planarity :  0.003   0.038   1463
  Dihedral  :  5.383  44.212   1178
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.03 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 29.71 %
    Favored  : 65.02 %
  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:  0.35 (0.26), residues: 1043
  helix:  1.79 (0.26), residues: 392
  sheet: -0.43 (0.32), residues: 225
  loop : -0.83 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 180 
 HIS   0.015   0.001   HIS R 292 
 PHE   0.020   0.001   PHE R 101 
 TYR   0.017   0.001   TYR A 391 
 ARG   0.003   0.000   ARG C  13 

*********************** 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
  233 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 186
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   26 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8867 (mtpp)
REVERT: B   70 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.7715 (m-80)
REVERT: B  306 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8181 (p0)
REVERT: C   18 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8375 (tp40)
REVERT: C   27 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.7071 (mmm-85)
REVERT: N    1 GLN cc_start: 0.7745 (pm20) cc_final: 0.7511 (pm20)
REVERT: N   13 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8478 (mm-40)
REVERT: N   73 ASP cc_start: 0.7516 (t0) cc_final: 0.7083 (t0)
REVERT: A  390 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7950 (tm-30)
REVERT: R   35 LYS cc_start: 0.8540 (ttpp) cc_final: 0.8312 (mtpt)
REVERT: R  258 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8047 (pp)
  outliers start: 47
  outliers final: 36
  residues processed: 214
  average time/residue: 0.2591
  time to fit residues: 77.8015
Evaluate side-chains
  221 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 180
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
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   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   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  107 CYS
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   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  169 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
Chi-restraints excluded: chain R residue  292 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 91 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 96 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 7 optimal weight:    0.1980
   chunk 92 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.3641 r_free = 0.3641 target = 0.127412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.102292 restraints weight = 13767.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.106355 restraints weight = 7370.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.109101 restraints weight = 4957.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8469  Z= 0.207
  Angle     :  0.628  13.347  11465  Z= 0.315
  Chirality :  0.042   0.141   1290
  Planarity :  0.003   0.039   1463
  Dihedral  :  5.368  43.837   1178
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.51 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 29.15 %
    Favored  : 65.02 %
  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:  0.33 (0.26), residues: 1043
  helix:  1.80 (0.26), residues: 393
  sheet: -0.49 (0.33), residues: 222
  loop : -0.83 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 180 
 HIS   0.017   0.001   HIS R 292 
 PHE   0.018   0.001   PHE R 101 
 TYR   0.017   0.001   TYR A 253 
 ARG   0.003   0.000   ARG C  13 

*********************** 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
  238 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 186
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   26 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8852 (mtpp)
REVERT: B   70 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.7686 (m-80)
REVERT: B  306 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8211 (p0)
REVERT: C   18 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8246 (tp40)
REVERT: C   21 MET cc_start: 0.8259 (tmm) cc_final: 0.7584 (tmm)
REVERT: C   22 GLU cc_start: 0.8537 (pp20) cc_final: 0.8294 (pp20)
REVERT: C   27 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.7104 (mmm-85)
REVERT: N   13 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8475 (mm-40)
REVERT: N   73 ASP cc_start: 0.7529 (t0) cc_final: 0.7089 (t0)
REVERT: R   35 LYS cc_start: 0.8503 (ttpp) cc_final: 0.8279 (mtpt)
REVERT: R  258 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8056 (pp)
  outliers start: 52
  outliers final: 40
  residues processed: 218
  average time/residue: 0.1897
  time to fit residues: 58.2747
Evaluate side-chains
  228 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 183
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
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  157 LEU
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  347 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   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  107 CYS
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   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  180 LEU
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
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:    0.5980
   chunk 40 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0000
   chunk 0 optimal weight:   10.0000
   chunk 25 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 53 optimal weight:    0.1980
   overall best weight:    0.4784

-------------------------------------------------------------------------------
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**
A 390 GLN
** 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 = 0.3661 r_free = 0.3661 target = 0.129042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.103967 restraints weight = 13713.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.108075 restraints weight = 7310.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.110862 restraints weight = 4897.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8469  Z= 0.185
  Angle     :  0.636  13.979  11465  Z= 0.319
  Chirality :  0.042   0.171   1290
  Planarity :  0.003   0.039   1463
  Dihedral  :  5.338  40.825   1178
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.31 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 30.16 %
    Favored  : 65.02 %
  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:  0.33 (0.26), residues: 1043
  helix:  1.78 (0.26), residues: 393
  sheet: -0.48 (0.33), residues: 227
  loop : -0.83 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 180 
 HIS   0.018   0.001   HIS R 292 
 PHE   0.016   0.001   PHE R 101 
 TYR   0.019   0.001   TYR A 391 
 ARG   0.003   0.000   ARG C  13 

*********************** 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
  233 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 190
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   26 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8851 (mtpp)
REVERT: B   70 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.7639 (m-80)
REVERT: B  306 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8316 (p0)
REVERT: C   18 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8251 (tp40)
REVERT: C   21 MET cc_start: 0.8284 (tmm) cc_final: 0.7631 (tmm)
REVERT: C   22 GLU cc_start: 0.8530 (pp20) cc_final: 0.8289 (pp20)
REVERT: C   27 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7069 (mmm-85)
REVERT: N   73 ASP cc_start: 0.7492 (t0) cc_final: 0.7071 (t0)
REVERT: A   60 MET cc_start: 0.6458 (pmm) cc_final: 0.6202 (pmm)
REVERT: A  390 GLN cc_start: 0.8184 (tm130) cc_final: 0.7979 (tm-30)
REVERT: R  258 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8077 (pp)
  outliers start: 43
  outliers final: 35
  residues processed: 212
  average time/residue: 0.2170
  time to fit residues: 64.3577
Evaluate side-chains
  223 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 183
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
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  110 TRP
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  236 HIS
Chi-restraints excluded: chain B residue  273 MET
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  347 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   27 ARG
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  107 CYS
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  301 VAL
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  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:    0.4980
   chunk 69 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 87 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0030
   chunk 34 optimal weight:    0.4980
   chunk 22 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.7392

-------------------------------------------------------------------------------
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 = 0.3662 r_free = 0.3662 target = 0.128545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.103803 restraints weight = 13658.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.107887 restraints weight = 7277.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.110592 restraints weight = 4865.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8469  Z= 0.216
  Angle     :  0.653  14.022  11465  Z= 0.328
  Chirality :  0.042   0.150   1290
  Planarity :  0.003   0.039   1463
  Dihedral  :  5.376  41.680   1178
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 31.05 %
    Favored  : 64.46 %
  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:  0.31 (0.26), residues: 1043
  helix:  1.76 (0.26), residues: 393
  sheet: -0.49 (0.33), residues: 227
  loop : -0.84 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 222 
 HIS   0.016   0.001   HIS R 292 
 PHE   0.016   0.001   PHE R 101 
 TYR   0.019   0.001   TYR A 391 
 ARG   0.003   0.000   ARG C  13 

********************** 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
  229 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 189
  time to evaluate  : 1.021 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   26 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8858 (mtpp)
REVERT: B   70 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.7618 (m-80)
REVERT: B  306 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8373 (p0)
REVERT: C   27 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7056 (mmm-85)
REVERT: N   73 ASP cc_start: 0.7554 (t0) cc_final: 0.7125 (t0)
REVERT: A  390 GLN cc_start: 0.8207 (tm130) cc_final: 0.7915 (tm-30)
REVERT: R  258 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8099 (pp)
  outliers start: 40
  outliers final: 35
  residues processed: 210
  average time/residue: 0.2217
  time to fit residues: 65.0963
Evaluate side-chains
  225 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 185
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
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  157 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  236 HIS
Chi-restraints excluded: chain B residue  273 MET
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  347 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   27 ARG
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  107 CYS
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  301 VAL
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  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 24 optimal weight:    0.8980
   chunk 101 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 82 optimal weight:    3.9990
   chunk 90 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
N  13 GLN
** 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 = 0.3661 r_free = 0.3661 target = 0.128574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.103579 restraints weight = 13734.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.107667 restraints weight = 7348.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.110390 restraints weight = 4935.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8469  Z= 0.213
  Angle     :  0.665  13.979  11465  Z= 0.331
  Chirality :  0.042   0.207   1290
  Planarity :  0.003   0.039   1463
  Dihedral  :  5.371  41.476   1178
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 31.28 %
    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:  0.31 (0.26), residues: 1043
  helix:  1.74 (0.27), residues: 393
  sheet: -0.46 (0.33), residues: 227
  loop : -0.83 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 180 
 HIS   0.014   0.001   HIS R 292 
 PHE   0.027   0.001   PHE A 340 
 TYR   0.018   0.001   TYR A 391 
 ARG   0.005   0.000   ARG A  13 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3103.11 seconds
wall clock time: 55 minutes 56.13 seconds (3356.13 seconds total)