Starting phenix.real_space_refine
on Wed Sep 17 11:11:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vhf_43236/09_2025/8vhf_43236.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vhf_43236/09_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_43236/09_2025/8vhf_43236.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vhf_43236/09_2025/8vhf_43236.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vhf_43236/09_2025/8vhf_43236.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vhf_43236/09_2025/8vhf_43236.cif"
  }
  resolution = 3.51
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.003 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.23, per 1000 atoms: 0.27
  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: 0.76
  Conformation dependent library (CDL) restraints added in 473.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.30
  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: 1.35

  Time building geometry restraints manager: 1.01 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:             2.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.960
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.107   8471  Z= 0.207
  Angle     :  0.823  16.485  11469  Z= 0.409
  Chirality :  0.044   0.226   1290
  Planarity :  0.004   0.074   1463
  Dihedral  : 17.720 119.958   3079
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 9.80
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (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
 ARG   0.010   0.000   ARG A  20 
 TYR   0.012   0.001   TYR B 275 
 PHE   0.031   0.001   PHE A 340 
 TRP   0.018   0.002   TRP B 180 
 HIS   0.010   0.001   HIS R 292 

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

*********************** 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  : 0.333 
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: 0.0963
  time to fit residues: 25.0022
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  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3671 r_free = 0.3671 target = 0.129900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.104410 restraints weight = 13630.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.108555 restraints weight = 7373.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.111276 restraints weight = 4969.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.113208 restraints weight = 3844.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.114323 restraints weight = 3217.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.0868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8471  Z= 0.140
  Angle     :  0.591  11.288  11469  Z= 0.298
  Chirality :  0.041   0.140   1290
  Planarity :  0.004   0.039   1463
  Dihedral  :  5.633  53.477   1178
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 28.81 %
    Favored  : 68.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.26), residues: 1043
  helix:  1.53 (0.26), residues: 404
  sheet: -0.31 (0.33), residues: 217
  loop : -1.03 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  13 
 TYR   0.010   0.001   TYR A 339 
 PHE   0.011   0.001   PHE A 376 
 TRP   0.013   0.001   TRP B 222 
 HIS   0.006   0.001   HIS B 236 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 8469)
  covalent geometry    : angle       0.59089 (11465)
  SS BOND              : bond        0.00136 (    2)
  SS BOND              : angle       0.63569 (    4)
  hydrogen bonds       : bond        0.03801 (  413)
  hydrogen bonds       : angle       4.87385 ( 1194)

*********************** 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
  219 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 194
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   70 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.7814 (m-80)
REVERT: B  300 TYR cc_start: 0.8352 (m-80) cc_final: 0.8117 (m-80)
REVERT: C   18 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8388 (tp40)
REVERT: C   27 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7205 (mmm-85)
REVERT: N   13 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8444 (mm-40)
REVERT: N   90 ASP cc_start: 0.8722 (t0) cc_final: 0.8419 (t0)
REVERT: A   27 GLU cc_start: 0.8659 (tp30) cc_final: 0.8420 (tp30)
REVERT: A  390 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7887 (tm-30)
REVERT: R  145 MET cc_start: 0.7748 (tpp) cc_final: 0.7357 (tpp)
  outliers start: 25
  outliers final: 16
  residues processed: 208
  average time/residue: 0.0884
  time to fit residues: 25.8990
Evaluate side-chains
  193 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 175
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
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   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 99 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 79 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 100 optimal weight:    0.1980
   chunk 38 optimal weight:    0.7980
   chunk 68 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
B  43 GLN
** 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 = 0.3670 r_free = 0.3670 target = 0.129729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.104585 restraints weight = 13418.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.108662 restraints weight = 7235.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.111355 restraints weight = 4872.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.113258 restraints weight = 3768.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.114499 restraints weight = 3156.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.1046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8471  Z= 0.129
  Angle     :  0.565   9.149  11469  Z= 0.288
  Chirality :  0.041   0.139   1290
  Planarity :  0.003   0.037   1463
  Dihedral  :  5.421  47.466   1178
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 29.15 %
    Favored  : 67.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.26), residues: 1043
  helix:  1.70 (0.26), residues: 403
  sheet: -0.30 (0.33), residues: 218
  loop : -0.98 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N  19 
 TYR   0.016   0.001   TYR A 391 
 PHE   0.013   0.001   PHE A 340 
 TRP   0.012   0.001   TRP B 180 
 HIS   0.007   0.001   HIS R 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8469)
  covalent geometry    : angle       0.56545 (11465)
  SS BOND              : bond        0.00120 (    2)
  SS BOND              : angle       0.43594 (    4)
  hydrogen bonds       : bond        0.03642 (  413)
  hydrogen bonds       : angle       4.70794 ( 1194)

*********************** 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
  220 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 189
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   70 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.7726 (m-80)
REVERT: C   18 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8436 (tp40)
REVERT: C   27 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.7290 (mmm-85)
REVERT: N   13 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8460 (mm-40)
REVERT: N   90 ASP cc_start: 0.8813 (t0) cc_final: 0.8520 (t0)
REVERT: A   27 GLU cc_start: 0.8640 (tp30) cc_final: 0.8390 (tp30)
REVERT: A  253 TYR cc_start: 0.5179 (p90) cc_final: 0.4573 (p90)
REVERT: A  390 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7906 (tm-30)
REVERT: R  145 MET cc_start: 0.7695 (tpp) cc_final: 0.7355 (tpp)
  outliers start: 31
  outliers final: 21
  residues processed: 206
  average time/residue: 0.0886
  time to fit residues: 25.7817
Evaluate side-chains
  200 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 177
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
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  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
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 77 optimal weight:    0.7980
   chunk 96 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 86 optimal weight:    0.8980
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
R 292 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.128842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.103709 restraints weight = 13667.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.107814 restraints weight = 7236.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.110630 restraints weight = 4849.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.112487 restraints weight = 3702.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.113483 restraints weight = 3091.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.1220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8471  Z= 0.136
  Angle     :  0.574  11.132  11469  Z= 0.291
  Chirality :  0.041   0.149   1290
  Planarity :  0.003   0.040   1463
  Dihedral  :  5.383  46.128   1178
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 27.80 %
    Favored  : 67.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.26), residues: 1043
  helix:  1.68 (0.26), residues: 404
  sheet: -0.33 (0.33), residues: 218
  loop : -1.02 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N  19 
 TYR   0.012   0.001   TYR A 391 
 PHE   0.015   0.001   PHE A 340 
 TRP   0.012   0.001   TRP B 180 
 HIS   0.012   0.001   HIS R 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 8469)
  covalent geometry    : angle       0.57417 (11465)
  SS BOND              : bond        0.00109 (    2)
  SS BOND              : angle       0.95959 (    4)
  hydrogen bonds       : bond        0.03617 (  413)
  hydrogen bonds       : angle       4.65356 ( 1194)

*********************** 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
  222 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 183
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   70 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.7756 (m-80)
REVERT: C   18 GLN cc_start: 0.8692 (tm-30) cc_final: 0.8415 (tp40)
REVERT: C   27 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.7247 (mmm-85)
REVERT: N   13 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8464 (mm-40)
REVERT: N   73 ASP cc_start: 0.7382 (t0) cc_final: 0.6896 (t70)
REVERT: N   90 ASP cc_start: 0.8863 (t0) cc_final: 0.8528 (t0)
REVERT: A   27 GLU cc_start: 0.8680 (tp30) cc_final: 0.8430 (tp30)
REVERT: A  253 TYR cc_start: 0.5434 (p90) cc_final: 0.5185 (p90)
REVERT: R  145 MET cc_start: 0.7752 (tpp) cc_final: 0.7449 (tpp)
REVERT: R  258 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7925 (pp)
REVERT: R  260 LEU cc_start: 0.8956 (tp) cc_final: 0.8696 (mp)
  outliers start: 39
  outliers final: 26
  residues processed: 209
  average time/residue: 0.0857
  time to fit residues: 25.2615
Evaluate side-chains
  202 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 173
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 LYS
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 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   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   39 VAL
Chi-restraints excluded: chain R residue   56 VAL
Chi-restraints excluded: chain R residue   97 MET
Chi-restraints excluded: chain R residue  102 ASP
Chi-restraints excluded: chain R residue  155 CYS
Chi-restraints excluded: chain R residue  169 LEU
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain R residue  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 87 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 25 optimal weight:    0.4980
   chunk 49 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 98 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  99 ASN
R 292 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.128751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.103662 restraints weight = 13542.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.107756 restraints weight = 7283.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.110507 restraints weight = 4898.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.112285 restraints weight = 3778.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.112762 restraints weight = 3180.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8471  Z= 0.136
  Angle     :  0.589   8.333  11469  Z= 0.298
  Chirality :  0.041   0.141   1290
  Planarity :  0.003   0.036   1463
  Dihedral  :  5.350  45.170   1178
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 28.81 %
    Favored  : 67.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.26), residues: 1043
  helix:  1.77 (0.26), residues: 400
  sheet: -0.33 (0.32), residues: 223
  loop : -0.99 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N  98 
 TYR   0.019   0.001   TYR A 391 
 PHE   0.016   0.001   PHE R 157 
 TRP   0.012   0.001   TRP B 180 
 HIS   0.013   0.001   HIS R 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8469)
  covalent geometry    : angle       0.58864 (11465)
  SS BOND              : bond        0.00091 (    2)
  SS BOND              : angle       1.23983 (    4)
  hydrogen bonds       : bond        0.03587 (  413)
  hydrogen bonds       : angle       4.62200 ( 1194)

*********************** 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
  221 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 184
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   70 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.7723 (m-80)
REVERT: C   18 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8406 (tp40)
REVERT: C   21 MET cc_start: 0.8371 (tmm) cc_final: 0.8168 (tmm)
REVERT: C   27 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.7221 (mmm-85)
REVERT: N   13 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8470 (mm-40)
REVERT: N   38 ARG cc_start: 0.8845 (ptt180) cc_final: 0.8629 (ptt180)
REVERT: N   73 ASP cc_start: 0.7432 (t0) cc_final: 0.7050 (t0)
REVERT: N   90 ASP cc_start: 0.8855 (t0) cc_final: 0.8606 (t0)
REVERT: A   27 GLU cc_start: 0.8666 (tp30) cc_final: 0.8418 (tp30)
REVERT: A  253 TYR cc_start: 0.5383 (p90) cc_final: 0.5155 (p90)
REVERT: A  390 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7918 (tm-30)
REVERT: R  145 MET cc_start: 0.7759 (tpp) cc_final: 0.7459 (tpp)
REVERT: R  258 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7987 (pp)
REVERT: R  260 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8713 (mp)
REVERT: R  284 LYS cc_start: 0.8930 (mmmt) cc_final: 0.8476 (mmmt)
  outliers start: 37
  outliers final: 27
  residues processed: 208
  average time/residue: 0.0905
  time to fit residues: 26.4352
Evaluate side-chains
  209 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 178
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 LYS
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   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   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  301 VAL
Chi-restraints excluded: chain A residue  348 ILE
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  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 98 optimal weight:    0.0570
   chunk 15 optimal weight:    0.6980
   chunk 33 optimal weight:    5.9990
   chunk 5 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 83 optimal weight:    0.0000
   chunk 77 optimal weight:    0.6980
   overall best weight:    0.4302

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

Flipped N/Q/H residues before XYZ refinement:
R 292 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.130943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.106120 restraints weight = 13461.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.110265 restraints weight = 7192.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.113080 restraints weight = 4813.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.114972 restraints weight = 3683.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.115991 restraints weight = 3071.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8471  Z= 0.113
  Angle     :  0.582  11.286  11469  Z= 0.290
  Chirality :  0.041   0.135   1290
  Planarity :  0.003   0.035   1463
  Dihedral  :  5.177  41.946   1178
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 28.70 %
    Favored  : 67.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.26), residues: 1043
  helix:  1.84 (0.26), residues: 400
  sheet: -0.39 (0.33), residues: 225
  loop : -0.94 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N  19 
 TYR   0.013   0.001   TYR A 391 
 PHE   0.018   0.001   PHE R 157 
 TRP   0.013   0.001   TRP B 180 
 HIS   0.009   0.001   HIS R 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 8469)
  covalent geometry    : angle       0.58137 (11465)
  SS BOND              : bond        0.00051 (    2)
  SS BOND              : angle       1.01894 (    4)
  hydrogen bonds       : bond        0.03454 (  413)
  hydrogen bonds       : angle       4.52891 ( 1194)

*********************** 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
  236 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 198
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   70 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.7612 (m-80)
REVERT: C   27 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.6984 (mmm-85)
REVERT: N   38 ARG cc_start: 0.8774 (ptt180) cc_final: 0.8550 (ptt180)
REVERT: N   73 ASP cc_start: 0.7461 (t0) cc_final: 0.7076 (t0)
REVERT: N   90 ASP cc_start: 0.8793 (t0) cc_final: 0.8555 (t0)
REVERT: A  262 GLN cc_start: 0.7928 (mp10) cc_final: 0.7698 (mp10)
REVERT: A  390 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7876 (tm-30)
REVERT: R  145 MET cc_start: 0.7713 (tpp) cc_final: 0.7409 (tpp)
REVERT: R  258 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.8023 (pp)
REVERT: R  260 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8674 (mp)
REVERT: R  284 LYS cc_start: 0.8822 (mmmt) cc_final: 0.8486 (mmmt)
  outliers start: 38
  outliers final: 26
  residues processed: 222
  average time/residue: 0.0915
  time to fit residues: 28.4442
Evaluate side-chains
  216 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 186
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue  110 TRP
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  236 HIS
Chi-restraints excluded: chain B residue  277 HIS
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain 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   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 A residue  348 ILE
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  169 LEU
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain R residue  258 LEU
Chi-restraints excluded: chain R residue  260 LEU
Chi-restraints excluded: chain R residue  266 LEU
Chi-restraints excluded: chain R residue  272 SER
Chi-restraints excluded: chain R residue  292 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 69 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 32 optimal weight:    0.4980
   chunk 47 optimal weight:    0.7980
   chunk 80 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 93 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0670
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
B 306 ASN
R 292 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.130068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.104972 restraints weight = 13743.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.109137 restraints weight = 7356.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.111894 restraints weight = 4928.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.113753 restraints weight = 3796.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.114920 restraints weight = 3175.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.1499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8471  Z= 0.128
  Angle     :  0.613  12.430  11469  Z= 0.306
  Chirality :  0.042   0.146   1290
  Planarity :  0.003   0.036   1463
  Dihedral  :  5.200  42.105   1178
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 29.48 %
    Favored  : 65.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.26), residues: 1043
  helix:  1.82 (0.26), residues: 400
  sheet: -0.39 (0.33), residues: 225
  loop : -0.91 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  13 
 TYR   0.013   0.001   TYR A 391 
 PHE   0.019   0.001   PHE A 340 
 TRP   0.012   0.001   TRP B 180 
 HIS   0.013   0.001   HIS R 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8469)
  covalent geometry    : angle       0.61268 (11465)
  SS BOND              : bond        0.00035 (    2)
  SS BOND              : angle       0.97327 (    4)
  hydrogen bonds       : bond        0.03492 (  413)
  hydrogen bonds       : angle       4.54981 ( 1194)

*********************** 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
  228 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 186
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   26 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8833 (mtpp)
REVERT: B   70 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.7640 (m-80)
REVERT: C   27 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.7102 (mmm-85)
REVERT: N   73 ASP cc_start: 0.7473 (t0) cc_final: 0.7093 (t0)
REVERT: A  215 ASP cc_start: 0.7543 (t70) cc_final: 0.7339 (t70)
REVERT: A  262 GLN cc_start: 0.7985 (mp10) cc_final: 0.7702 (mp10)
REVERT: R  145 MET cc_start: 0.7757 (tpp) cc_final: 0.7451 (tpp)
REVERT: R  258 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8029 (pp)
REVERT: R  260 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8681 (mp)
  outliers start: 42
  outliers final: 33
  residues processed: 211
  average time/residue: 0.0875
  time to fit residues: 26.2143
Evaluate side-chains
  221 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 183
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 LYS
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue  110 TRP
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  266 LEU
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 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   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  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   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  224 LEU
Chi-restraints excluded: chain R residue  258 LEU
Chi-restraints excluded: chain R residue  260 LEU
Chi-restraints excluded: chain R residue  266 LEU
Chi-restraints excluded: chain R residue  272 SER
Chi-restraints excluded: chain R residue  292 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 79 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B 306 ASN
** 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 = 0.3653 r_free = 0.3653 target = 0.128220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.103129 restraints weight = 13484.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.107188 restraints weight = 7295.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.109903 restraints weight = 4940.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.111769 restraints weight = 3826.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.112981 restraints weight = 3200.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8471  Z= 0.148
  Angle     :  0.631  13.796  11469  Z= 0.314
  Chirality :  0.042   0.138   1290
  Planarity :  0.003   0.036   1463
  Dihedral  :  5.341  42.113   1178
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 30.04 %
    Favored  : 65.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.26), residues: 1043
  helix:  1.78 (0.26), residues: 400
  sheet: -0.36 (0.33), residues: 215
  loop : -0.92 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  13 
 TYR   0.014   0.001   TYR A 391 
 PHE   0.026   0.001   PHE A 340 
 TRP   0.011   0.001   TRP B 180 
 HIS   0.016   0.001   HIS R 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 8469)
  covalent geometry    : angle       0.63055 (11465)
  SS BOND              : bond        0.00038 (    2)
  SS BOND              : angle       1.05062 (    4)
  hydrogen bonds       : bond        0.03590 (  413)
  hydrogen bonds       : angle       4.60930 ( 1194)

*********************** 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
  228 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 186
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   26 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8845 (mtpp)
REVERT: B   70 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.7656 (m-80)
REVERT: B  300 TYR cc_start: 0.8535 (m-10) cc_final: 0.8010 (m-80)
REVERT: C   18 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8396 (tp40)
REVERT: C   27 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.7171 (mmm-85)
REVERT: N   73 ASP cc_start: 0.7537 (t0) cc_final: 0.7166 (t0)
REVERT: A  215 ASP cc_start: 0.7654 (t70) cc_final: 0.7437 (t70)
REVERT: A  390 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7950 (tm-30)
REVERT: R  258 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8046 (pp)
REVERT: R  260 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8712 (mp)
REVERT: R  284 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8776 (mmmt)
  outliers start: 42
  outliers final: 34
  residues processed: 211
  average time/residue: 0.0862
  time to fit residues: 25.9772
Evaluate side-chains
  220 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 181
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 LYS
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  266 LEU
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 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  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   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  224 LEU
Chi-restraints excluded: chain R residue  239 THR
Chi-restraints excluded: chain R residue  258 LEU
Chi-restraints excluded: chain R residue  260 LEU
Chi-restraints excluded: chain R residue  266 LEU
Chi-restraints excluded: chain R residue  272 SER
Chi-restraints excluded: chain R residue  292 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0870
   chunk 94 optimal weight:    6.9990
   chunk 68 optimal weight:    0.6980
   chunk 79 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.7160

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3659 r_free = 0.3659 target = 0.128828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.103664 restraints weight = 13566.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.107739 restraints weight = 7330.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.110481 restraints weight = 4955.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.112322 restraints weight = 3837.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.113578 restraints weight = 3219.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8471  Z= 0.139
  Angle     :  0.640  14.696  11469  Z= 0.319
  Chirality :  0.042   0.137   1290
  Planarity :  0.003   0.037   1463
  Dihedral  :  5.336  41.580   1178
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 30.49 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.26), residues: 1043
  helix:  1.81 (0.26), residues: 399
  sheet: -0.40 (0.33), residues: 220
  loop : -0.91 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  13 
 TYR   0.020   0.001   TYR A 391 
 PHE   0.028   0.001   PHE A 340 
 TRP   0.011   0.001   TRP B 180 
 HIS   0.018   0.001   HIS R 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8469)
  covalent geometry    : angle       0.63974 (11465)
  SS BOND              : bond        0.00038 (    2)
  SS BOND              : angle       0.98036 (    4)
  hydrogen bonds       : bond        0.03568 (  413)
  hydrogen bonds       : angle       4.62979 ( 1194)

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

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

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

  2086 Ramachandran restraints generated.
    1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 190
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   26 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8860 (mtpp)
REVERT: B   70 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.7670 (m-80)
REVERT: B  300 TYR cc_start: 0.8557 (m-10) cc_final: 0.8065 (m-80)
REVERT: C   18 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8446 (tp40)
REVERT: C   27 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7146 (mmm-85)
REVERT: N   73 ASP cc_start: 0.7532 (t0) cc_final: 0.7175 (t0)
REVERT: A  215 ASP cc_start: 0.7684 (t70) cc_final: 0.7467 (t70)
REVERT: A  262 GLN cc_start: 0.7869 (mp10) cc_final: 0.7660 (mp10)
REVERT: A  390 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7952 (tm-30)
REVERT: R  258 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8085 (pp)
REVERT: R  260 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8724 (mp)
  outliers start: 40
  outliers final: 32
  residues processed: 212
  average time/residue: 0.0874
  time to fit residues: 26.3900
Evaluate side-chains
  224 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 187
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 LYS
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  266 LEU
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 B residue  350 TRP
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  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   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  224 LEU
Chi-restraints excluded: chain R residue  258 LEU
Chi-restraints excluded: chain R residue  260 LEU
Chi-restraints excluded: chain R residue  266 LEU
Chi-restraints excluded: chain R residue  272 SER
Chi-restraints excluded: chain R residue  292 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0770
   chunk 92 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 81 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.9140

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3647 r_free = 0.3647 target = 0.127861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.102634 restraints weight = 13566.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.106666 restraints weight = 7360.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.109397 restraints weight = 4993.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.111233 restraints weight = 3874.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.112292 restraints weight = 3256.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8471  Z= 0.155
  Angle     :  0.651  14.736  11469  Z= 0.324
  Chirality :  0.042   0.140   1290
  Planarity :  0.003   0.037   1463
  Dihedral  :  5.404  42.280   1178
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 30.49 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.26), residues: 1043
  helix:  1.77 (0.26), residues: 399
  sheet: -0.46 (0.32), residues: 225
  loop : -0.89 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  13 
 TYR   0.025   0.001   TYR A 391 
 PHE   0.024   0.001   PHE A 340 
 TRP   0.010   0.001   TRP B 222 
 HIS   0.014   0.001   HIS R 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 8469)
  covalent geometry    : angle       0.65076 (11465)
  SS BOND              : bond        0.00047 (    2)
  SS BOND              : angle       1.05483 (    4)
  hydrogen bonds       : bond        0.03615 (  413)
  hydrogen bonds       : angle       4.67378 ( 1194)

********************** 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
  226 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 186
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   26 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8856 (mtpp)
REVERT: B   70 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.7725 (m-80)
REVERT: B  300 TYR cc_start: 0.8596 (m-10) cc_final: 0.8072 (m-80)
REVERT: C   18 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8448 (tp40)
REVERT: C   27 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.7236 (mmm-85)
REVERT: N   73 ASP cc_start: 0.7563 (t0) cc_final: 0.7199 (t0)
REVERT: A   60 MET cc_start: 0.6576 (pmm) cc_final: 0.6335 (pmm)
REVERT: A  215 ASP cc_start: 0.7666 (t70) cc_final: 0.7447 (t70)
REVERT: A  253 TYR cc_start: 0.5172 (p90) cc_final: 0.4747 (p90)
REVERT: A  390 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7983 (tm-30)
REVERT: R  258 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8068 (pp)
REVERT: R  260 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8761 (mp)
  outliers start: 40
  outliers final: 33
  residues processed: 211
  average time/residue: 0.0892
  time to fit residues: 26.4697
Evaluate side-chains
  223 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 185
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 LYS
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  266 LEU
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 B residue  350 TRP
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  112 SER
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 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  224 LEU
Chi-restraints excluded: chain R residue  239 THR
Chi-restraints excluded: chain R residue  258 LEU
Chi-restraints excluded: chain R residue  260 LEU
Chi-restraints excluded: chain R residue  266 LEU
Chi-restraints excluded: chain R residue  272 SER
Chi-restraints excluded: chain R residue  292 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 66 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9990
   chunk 9 optimal weight:    0.4980
   chunk 87 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   chunk 86 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3661 r_free = 0.3661 target = 0.128900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.103721 restraints weight = 13648.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.107822 restraints weight = 7346.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.110583 restraints weight = 4946.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.112430 restraints weight = 3818.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.113486 restraints weight = 3199.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8471  Z= 0.138
  Angle     :  0.651  14.800  11469  Z= 0.324
  Chirality :  0.042   0.136   1290
  Planarity :  0.003   0.037   1463
  Dihedral  :  5.363  41.130   1178
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 30.49 %
    Favored  : 64.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.26), residues: 1043
  helix:  1.78 (0.26), residues: 399
  sheet: -0.42 (0.32), residues: 227
  loop : -0.90 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  13 
 TYR   0.027   0.001   TYR A 391 
 PHE   0.022   0.001   PHE A 340 
 TRP   0.011   0.001   TRP B 180 
 HIS   0.016   0.001   HIS R 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 8469)
  covalent geometry    : angle       0.65135 (11465)
  SS BOND              : bond        0.00047 (    2)
  SS BOND              : angle       0.95048 (    4)
  hydrogen bonds       : bond        0.03555 (  413)
  hydrogen bonds       : angle       4.65831 ( 1194)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1637.93 seconds
wall clock time: 29 minutes 11.72 seconds (1751.72 seconds total)