Starting phenix.real_space_refine
on Thu Jun 12 10:23:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u8f_42023/06_2025/8u8f_42023_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u8f_42023/06_2025/8u8f_42023.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u8f_42023/06_2025/8u8f_42023.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u8f_42023/06_2025/8u8f_42023.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u8f_42023/06_2025/8u8f_42023_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u8f_42023/06_2025/8u8f_42023_trim.cif"
  }
  resolution = 3.49
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.003 sd=   0.065
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    4433      2.51       5
     N    1209      2.21       5
     O    1275      1.98       5
     H    6925      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13891
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 3800
          Classifications: {'peptide': 231}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 5094
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 5094
          Classifications: {'peptide': 337}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
    Chain: "G"
      Number of atoms: 871
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 871
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "R"
      Number of atoms: 4094
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 4094
          Classifications: {'peptide': 265}
          Link IDs: {'PTRANS': 10, 'TRANS': 254}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 32
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1, 16
          Unusual residues: {'PLM': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'PLM:plan-1': 1}
          Unresolved non-hydrogen planarities: 2
      Conformer: "B"
        Number of residues, atoms: 1, 16
          Unusual residues: {'PLM': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'PLM:plan-1': 1}
          Unresolved non-hydrogen planarities: 2
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" CA APLM R 401 " occ=0.68
      ... (30 atoms not shown)
      pdb=" CF BPLM R 401 " occ=0.32
  Time building chain proxies: 6.68, per 1000 atoms: 0.48
  Number of scatterers: 13891
  At special positions: 0
  Unit cell: (78.26, 100.62, 126.42, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      49     16.00
     O    1275      8.00
     N    1209      7.00
     C    4433      6.00
     H    6925      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 177 " - pdb=" SG  CYS R 184 " distance=2.04

  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: 3.49
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1670

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      46.1% alpha, 16.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 38
      removed outlier: 3.552A  pdb=" N   LYS A  28 " --> pdb=" O   LYS A  24 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 233 through 239
    Processing helix  chain 'A' and resid 264 through 279
      removed outlier: 4.130A  pdb=" N   ALA A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.533A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.093A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.799A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.999A  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 'B' and resid 5 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 8 through 24
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.565A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 44 through 68
      removed outlier: 3.691A  pdb=" N   CYS R  48 " --> pdb=" O   ASP R  44 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU R  60 " --> pdb=" O   CYS R  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 73 through 101
      removed outlier: 3.649A  pdb=" N   PHE R 101 " --> pdb=" O   PHE R  97 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 105 through 140
      removed outlier: 3.610A  pdb=" N   SER R 109 " --> pdb=" O   SER R 105 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   LEU R 110 " --> pdb=" O   ALA R 106 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   VAL R 111 " --> pdb=" O   GLU R 107 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 142 through 146
      removed outlier: 4.059A  pdb=" N   TYR R 145 " --> pdb=" O   LEU R 142 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 147 through 170
      removed outlier: 4.035A  pdb=" N   LEU R 170 " --> pdb=" O   GLY R 166 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 191 through 230
      removed outlier: 3.549A  pdb=" N   LEU R 229 " --> pdb=" O   GLN R 225 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   GLN R 230 " --> pdb=" O   GLN R 226 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 244 through 253
      removed outlier: 3.655A  pdb=" N   VAL R 251 " --> pdb=" O   ALA R 247 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 254 through 270
      Proline residue:  R 262  - end of helix
    Processing helix  chain 'R' and resid 275 through 282
      removed outlier: 4.236A  pdb=" N   THR R 279 " --> pdb=" O   PRO R 275 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   TYR R 280 " --> pdb=" O   PRO R 276 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 282 through 298
      removed outlier: 3.772A  pdb=" N   ALA R 286 " --> pdb=" O   THR R 282 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASN R 289 " --> pdb=" O   PRO R 285 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   SER R 290 " --> pdb=" O   ALA R 286 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   MET R 291 " --> pdb=" O   THR R 287 " (cutoff:3.500A)
      Proline residue:  R 294  - end of helix
    Processing helix  chain 'R' and resid 301 through 313
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.518A  pdb=" N   PHE A 208 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ASP A 223 " --> pdb=" O   PHE A 208 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   LEU A  45 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50
      removed outlier: 3.790A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.901A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.394A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.533A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.627A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.857A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.205A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LEU B 210 " --> pdb=" O   GLN B 220 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234
      removed outlier: 3.837A  pdb=" N   CYS B 233 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.484A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.317A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)

    363 hydrogen bonds defined for protein.
    1053 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: 5.51

  Time building geometry restraints manager: 4.25 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 6897
        1.04 -     1.23: 246
        1.23 -     1.43: 2748
        1.43 -     1.63: 4065
        1.63 -     1.83: 68
  Bond restraints: 14024
  Sorted by residual:
  bond pdb=" N   VAL R 132 "
       pdb=" CA  VAL R 132 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.30e-02 5.92e+03 8.90e+00
  bond pdb=" N   LEU R 136 "
       pdb=" H   LEU R 136 "
    ideal  model  delta    sigma   weight residual
    0.860  0.912 -0.052 2.00e-02 2.50e+03 6.83e+00
  bond pdb=" N   ALA R 129 "
       pdb=" H   ALA R 129 "
    ideal  model  delta    sigma   weight residual
    0.860  0.912 -0.052 2.00e-02 2.50e+03 6.74e+00
  bond pdb=" N   VAL R 155 "
       pdb=" H   VAL R 155 "
    ideal  model  delta    sigma   weight residual
    0.860  0.912 -0.052 2.00e-02 2.50e+03 6.73e+00
  bond pdb=" N   LEU R  78 "
       pdb=" H   LEU R  78 "
    ideal  model  delta    sigma   weight residual
    0.860  0.912 -0.052 2.00e-02 2.50e+03 6.70e+00
  ... (remaining 14019 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.09: 25239
        7.09 -    14.18: 2
       14.18 -    21.27: 0
       21.27 -    28.36: 0
       28.36 -    35.45: 3
  Bond angle restraints: 25244
  Sorted by residual:
  angle pdb=" C   ASN B 340 "
        pdb=" CA  ASN B 340 "
        pdb=" HA  ASN B 340 "
      ideal   model   delta    sigma   weight residual
     109.00   73.55   35.45 3.00e+00 1.11e-01 1.40e+02
  angle pdb=" N   ASN B 340 "
        pdb=" CA  ASN B 340 "
        pdb=" HA  ASN B 340 "
      ideal   model   delta    sigma   weight residual
     110.00   74.70   35.30 3.00e+00 1.11e-01 1.38e+02
  angle pdb=" CB  ASN B 340 "
        pdb=" CA  ASN B 340 "
        pdb=" HA  ASN B 340 "
      ideal   model   delta    sigma   weight residual
     109.00   79.73   29.27 3.00e+00 1.11e-01 9.52e+01
  angle pdb=" CA  PRO G  49 "
        pdb=" N   PRO G  49 "
        pdb=" CD  PRO G  49 "
      ideal   model   delta    sigma   weight residual
     112.00  104.99    7.01 1.40e+00 5.10e-01 2.51e+01
  angle pdb=" N   ASN B 313 "
        pdb=" CA  ASN B 313 "
        pdb=" CB  ASN B 313 "
      ideal   model   delta    sigma   weight residual
     114.17  109.59    4.58 1.14e+00 7.69e-01 1.62e+01
  ... (remaining 25239 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 5908
       17.91 -    35.83: 502
       35.83 -    53.74: 143
       53.74 -    71.66: 36
       71.66 -    89.57: 14
  Dihedral angle restraints: 6603
    sinusoidal: 3564
      harmonic: 3039
  Sorted by residual:
  dihedral pdb=" CB  CYS R 177 "
           pdb=" SG  CYS R 177 "
           pdb=" SG  CYS R 184 "
           pdb=" CB  CYS R 184 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -26.65  -59.35     1      1.00e+01 1.00e-02 4.71e+01
  dihedral pdb=" CA  ASN R 176 "
           pdb=" C   ASN R 176 "
           pdb=" N   CYS R 177 "
           pdb=" CA  CYS R 177 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.38   21.62     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  VAL R 187 "
           pdb=" C   VAL R 187 "
           pdb=" N   TYR R 188 "
           pdb=" CA  TYR R 188 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.61  -18.39     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 6600 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 1050
       0.091 -    0.182: 53
       0.182 -    0.273: 0
       0.273 -    0.364: 0
       0.364 -    0.455: 1
  Chirality restraints: 1104
  Sorted by residual:
  chirality pdb=" CA  ASN B 340 "
            pdb=" N   ASN B 340 "
            pdb=" C   ASN B 340 "
            pdb=" CB  ASN B 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.17e+00
  chirality pdb=" CA  VAL R 155 "
            pdb=" N   VAL R 155 "
            pdb=" C   VAL R 155 "
            pdb=" CB  VAL R 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.22e-01
  chirality pdb=" CA  LEU R 159 "
            pdb=" N   LEU R 159 "
            pdb=" C   LEU R 159 "
            pdb=" CB  LEU R 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.83e-01
  ... (remaining 1101 not shown)

  Planarity restraints: 2076
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG R 152 "    0.447 9.50e-02 1.11e+02   1.51e-01 3.60e+01
        pdb=" NE  ARG R 152 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  ARG R 152 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG R 152 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG R 152 "   -0.005 2.00e-02 2.50e+03
        pdb="HH11 ARG R 152 "   -0.048 2.00e-02 2.50e+03
        pdb="HH12 ARG R 152 "    0.051 2.00e-02 2.50e+03
        pdb="HH21 ARG R 152 "    0.011 2.00e-02 2.50e+03
        pdb="HH22 ARG R 152 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "    0.085 5.00e-02 4.00e+02   1.25e-01 2.51e+01
        pdb=" N   PRO G  49 "   -0.217 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "    0.065 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "    0.066 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 136 "    0.013 2.00e-02 2.50e+03   2.41e-02 5.82e+00
        pdb=" N   SER R 137 "   -0.042 2.00e-02 2.50e+03
        pdb=" CA  SER R 137 "    0.011 2.00e-02 2.50e+03
        pdb=" H   SER R 137 "    0.018 2.00e-02 2.50e+03
  ... (remaining 2073 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 912
        2.20 -     2.80: 28548
        2.80 -     3.40: 38690
        3.40 -     4.00: 49337
        4.00 -     4.60: 76825
  Nonbonded interactions: 194312
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN R 176 "
            pdb=" H   SER R 191 "
     model   vdw
     1.600 2.450
  nonbonded pdb=" O   ASN R 140 "
            pdb=" H   TYR R 144 "
     model   vdw
     1.634 2.450
  nonbonded pdb=" OD1 ASP R 179 "
            pdb=" H   LEU R 181 "
     model   vdw
     1.662 2.450
  nonbonded pdb="HH21 ARG A  38 "
            pdb=" OE2 GLU R 147 "
     model   vdw
     1.666 2.450
  nonbonded pdb=" H   PHE B 235 "
            pdb=" O   ALA B 240 "
     model   vdw
     1.666 2.450
  ... (remaining 194307 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.670
  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:             0.230
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.090
  Set scattering table:                    0.140
  Process input model:                     31.850
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6712
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      :  0.003   0.109   7100  Z= 0.172
  Angle     :  0.545  10.634   9618  Z= 0.326
  Chirality :  0.042   0.455   1104
  Planarity :  0.007   0.182   1219
  Dihedral  : 15.464  89.571   2563
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.51 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  : 19.46 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.30), residues: 875
  helix:  2.63 (0.28), residues: 358
  sheet:  0.14 (0.42), residues: 156
  loop : -0.42 (0.35), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  63 
 HIS   0.002   0.000   HIS R 223 
 PHE   0.013   0.001   PHE R 299 
 TYR   0.024   0.001   TYR R 139 
 ARG   0.004   0.000   ARG B  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17459 (  363)
  hydrogen bonds       : angle       7.02043 ( 1053)
  SS BOND              : bond        0.01154 (    1)
  SS BOND              : angle       1.38070 (    2)
  covalent geometry    : bond        0.00323 ( 7099)
  covalent geometry    : angle       0.54445 ( 9616)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  139 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 139
  average time/residue: 0.4664
  time to fit residues: 84.3052
Evaluate side-chains
  132 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  234 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.188774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.153117 restraints weight = 24477.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 3.04
r_work: 0.3765 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3768
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3768 r_free = 0.3768    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3768 r_free = 0.3768    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3768
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7100  Z= 0.170
  Angle     :  0.548  10.162   9618  Z= 0.297
  Chirality :  0.042   0.444   1104
  Planarity :  0.005   0.078   1219
  Dihedral  :  4.757  51.558    992
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.34 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 17.99 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.30), residues: 875
  helix:  2.49 (0.27), residues: 368
  sheet: -0.67 (0.43), residues: 162
  loop : -0.69 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  63 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.019   0.002   PHE A 246 
 TYR   0.014   0.001   TYR B 124 
 ARG   0.007   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04766 (  363)
  hydrogen bonds       : angle       4.91131 ( 1053)
  SS BOND              : bond        0.01220 (    1)
  SS BOND              : angle       2.19878 (    2)
  covalent geometry    : bond        0.00370 ( 7099)
  covalent geometry    : angle       0.54681 ( 9616)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  157 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 140
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   63 TRP cc_start: 0.7444 (m-10) cc_final: 0.7124 (m-10)
REVERT: G   17 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8134 (mm-30)
REVERT: R   56 CYS cc_start: 0.7749 (OUTLIER) cc_final: 0.6991 (m)
REVERT: R  145 TYR cc_start: 0.7480 (m-80) cc_final: 0.7052 (m-80)
REVERT: R  179 ASP cc_start: 0.6923 (p0) cc_final: 0.6535 (t0)
  outliers start: 17
  outliers final: 12
  residues processed: 150
  average time/residue: 0.4673
  time to fit residues: 91.5904
Evaluate side-chains
  147 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 134
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue   56 CYS
Chi-restraints excluded: chain R residue   68 THR
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  170 LEU
Chi-restraints excluded: chain R residue  309 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 60 optimal weight:   10.0000
   chunk 53 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 16 optimal weight:    0.2980
   chunk 64 optimal weight:    0.6980
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.187384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.151752 restraints weight = 24470.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3888 rms_B_bonded: 3.01
r_work: 0.3750 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3750
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3750 r_free = 0.3750    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3750 r_free = 0.3750    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3750
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   7100  Z= 0.136
  Angle     :  0.508  10.157   9618  Z= 0.273
  Chirality :  0.041   0.441   1104
  Planarity :  0.004   0.067   1219
  Dihedral  :  4.665  49.901    992
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.43 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 18.39 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.30), residues: 875
  helix:  2.57 (0.27), residues: 366
  sheet: -1.08 (0.40), residues: 172
  loop : -0.72 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  63 
 HIS   0.003   0.001   HIS R 223 
 PHE   0.014   0.001   PHE B 241 
 TYR   0.013   0.001   TYR A 311 
 ARG   0.010   0.000   ARG R 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04310 (  363)
  hydrogen bonds       : angle       4.59683 ( 1053)
  SS BOND              : bond        0.01145 (    1)
  SS BOND              : angle       2.06059 (    2)
  covalent geometry    : bond        0.00291 ( 7099)
  covalent geometry    : angle       0.50762 ( 9616)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  156 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 1.063 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 TYR cc_start: 0.7991 (m-80) cc_final: 0.7705 (m-80)
REVERT: B   44 GLN cc_start: 0.7372 (mt0) cc_final: 0.7032 (mt0)
REVERT: B   63 TRP cc_start: 0.7513 (m-10) cc_final: 0.7152 (m-10)
REVERT: B  258 ASP cc_start: 0.7191 (t70) cc_final: 0.6680 (t70)
REVERT: G   13 ARG cc_start: 0.8400 (ttm110) cc_final: 0.8164 (ttm110)
REVERT: G   17 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8214 (mm-30)
REVERT: R   56 CYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7015 (m)
REVERT: R  179 ASP cc_start: 0.6919 (p0) cc_final: 0.6480 (t70)
REVERT: R  204 MET cc_start: 0.7368 (ttm) cc_final: 0.7160 (mtp)
  outliers start: 21
  outliers final: 13
  residues processed: 150
  average time/residue: 0.4651
  time to fit residues: 90.0992
Evaluate side-chains
  146 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  237 CYS
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue   56 CYS
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  284 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 45 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 24 optimal weight:    8.9990
   chunk 20 optimal weight:    0.2980
   chunk 38 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.183676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.147993 restraints weight = 24535.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 3.00
r_work: 0.3706 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3708
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3708 r_free = 0.3708    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3708 r_free = 0.3708    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3708
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   7100  Z= 0.174
  Angle     :  0.547  10.079   9618  Z= 0.295
  Chirality :  0.042   0.437   1104
  Planarity :  0.004   0.065   1219
  Dihedral  :  5.071  48.493    992
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.26 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 19.19 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.29), residues: 875
  helix:  2.33 (0.27), residues: 366
  sheet: -1.43 (0.40), residues: 170
  loop : -0.89 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  63 
 HIS   0.004   0.001   HIS R 223 
 PHE   0.021   0.002   PHE B 241 
 TYR   0.009   0.001   TYR R 213 
 ARG   0.004   0.000   ARG B 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04364 (  363)
  hydrogen bonds       : angle       4.60548 ( 1053)
  SS BOND              : bond        0.01032 (    1)
  SS BOND              : angle       2.27549 (    2)
  covalent geometry    : bond        0.00381 ( 7099)
  covalent geometry    : angle       0.54617 ( 9616)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  161 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.7618 (tpp80) cc_final: 0.7327 (tpp80)
REVERT: B   44 GLN cc_start: 0.7397 (mt0) cc_final: 0.7080 (mt0)
REVERT: B   63 TRP cc_start: 0.7482 (m-10) cc_final: 0.6889 (m-10)
REVERT: B  262 MET cc_start: 0.7632 (tpp) cc_final: 0.7305 (tpp)
REVERT: G   17 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8274 (mm-30)
REVERT: R   56 CYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7063 (m)
REVERT: R  179 ASP cc_start: 0.6919 (p0) cc_final: 0.6404 (t70)
REVERT: R  204 MET cc_start: 0.7407 (ttm) cc_final: 0.7188 (mtp)
  outliers start: 25
  outliers final: 20
  residues processed: 151
  average time/residue: 0.4791
  time to fit residues: 94.4897
Evaluate side-chains
  152 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue   56 CYS
Chi-restraints excluded: chain R residue   68 THR
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  170 LEU
Chi-restraints excluded: chain R residue  191 SER
Chi-restraints excluded: chain R residue  261 LEU
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  309 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 23 optimal weight:   10.0000
   chunk 7 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 80 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    1.3788

-------------------------------------------------------------------------------
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 = 0.4217 r_free = 0.4217 target = 0.184360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.148481 restraints weight = 24727.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 3.03
r_work: 0.3714 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3706
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3706 r_free = 0.3706    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3706 r_free = 0.3706    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3706
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7100  Z= 0.151
  Angle     :  0.527  10.016   9618  Z= 0.284
  Chirality :  0.041   0.438   1104
  Planarity :  0.004   0.061   1219
  Dihedral  :  4.954  47.494    992
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 20.27 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.29), residues: 875
  helix:  2.36 (0.27), residues: 366
  sheet: -1.59 (0.41), residues: 165
  loop : -0.98 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  63 
 HIS   0.004   0.001   HIS R 223 
 PHE   0.021   0.002   PHE A 290 
 TYR   0.013   0.001   TYR A 311 
 ARG   0.010   0.000   ARG R 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04145 (  363)
  hydrogen bonds       : angle       4.52539 ( 1053)
  SS BOND              : bond        0.00974 (    1)
  SS BOND              : angle       2.05784 (    2)
  covalent geometry    : bond        0.00329 ( 7099)
  covalent geometry    : angle       0.52655 ( 9616)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  155 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.7581 (tpp80) cc_final: 0.7328 (tpp80)
REVERT: A  358 TYR cc_start: 0.8046 (m-80) cc_final: 0.7704 (m-80)
REVERT: B   63 TRP cc_start: 0.7437 (m-10) cc_final: 0.6871 (m-10)
REVERT: R   56 CYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7032 (m)
REVERT: R  179 ASP cc_start: 0.7033 (p0) cc_final: 0.6488 (t70)
REVERT: R  204 MET cc_start: 0.7389 (ttm) cc_final: 0.7182 (mtp)
  outliers start: 23
  outliers final: 19
  residues processed: 147
  average time/residue: 0.4603
  time to fit residues: 87.2925
Evaluate side-chains
  151 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  237 CYS
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain R residue   56 CYS
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  191 SER
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  309 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 56 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.179116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.143437 restraints weight = 24914.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3802 rms_B_bonded: 2.99
r_work: 0.3662 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3675
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7100  Z= 0.238
  Angle     :  0.613  10.073   9618  Z= 0.335
  Chirality :  0.044   0.432   1104
  Planarity :  0.005   0.062   1219
  Dihedral  :  5.574  46.603    992
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.63 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 19.87 %
    Favored  : 75.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.29), residues: 875
  helix:  1.84 (0.27), residues: 369
  sheet: -1.92 (0.40), residues: 161
  loop : -1.28 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  63 
 HIS   0.006   0.001   HIS R 223 
 PHE   0.028   0.002   PHE B 241 
 TYR   0.012   0.002   TYR B 264 
 ARG   0.008   0.001   ARG R 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04710 (  363)
  hydrogen bonds       : angle       4.84289 ( 1053)
  SS BOND              : bond        0.00998 (    1)
  SS BOND              : angle       2.74513 (    2)
  covalent geometry    : bond        0.00531 ( 7099)
  covalent geometry    : angle       0.61213 ( 9616)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  167 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 134
  time to evaluate  : 1.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.7688 (tpp80) cc_final: 0.7417 (tpp80)
REVERT: A  205 SER cc_start: 0.6286 (OUTLIER) cc_final: 0.6082 (t)
REVERT: A  358 TYR cc_start: 0.8112 (m-80) cc_final: 0.7817 (m-80)
REVERT: B   63 TRP cc_start: 0.7468 (m-10) cc_final: 0.6847 (m-10)
REVERT: B  262 MET cc_start: 0.7656 (tpp) cc_final: 0.7289 (tpp)
REVERT: R   56 CYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7094 (m)
  outliers start: 33
  outliers final: 26
  residues processed: 153
  average time/residue: 0.4671
  time to fit residues: 92.2191
Evaluate side-chains
  157 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 129
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  237 CYS
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain R residue   56 CYS
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  115 VAL
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  191 SER
Chi-restraints excluded: chain R residue  226 GLN
Chi-restraints excluded: chain R residue  261 LEU
Chi-restraints excluded: chain R residue  281 LEU
Chi-restraints excluded: chain R residue  309 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 16 optimal weight:    7.9990
   chunk 54 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
B 155 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.182428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.146816 restraints weight = 24767.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3832 rms_B_bonded: 2.99
r_work: 0.3694 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3704
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3704 r_free = 0.3704    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3704 r_free = 0.3704    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3704
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7100  Z= 0.154
  Angle     :  0.540   9.912   9618  Z= 0.292
  Chirality :  0.042   0.437   1104
  Planarity :  0.005   0.068   1219
  Dihedral  :  5.192  45.885    992
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 21.74 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.29), residues: 875
  helix:  2.09 (0.27), residues: 367
  sheet: -1.89 (0.40), residues: 166
  loop : -1.20 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 281 
 HIS   0.004   0.001   HIS R 223 
 PHE   0.017   0.001   PHE B 241 
 TYR   0.013   0.001   TYR A 311 
 ARG   0.011   0.001   ARG R 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04208 (  363)
  hydrogen bonds       : angle       4.59698 ( 1053)
  SS BOND              : bond        0.00910 (    1)
  SS BOND              : angle       1.96427 (    2)
  covalent geometry    : bond        0.00336 ( 7099)
  covalent geometry    : angle       0.53931 ( 9616)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  151 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 1.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.7637 (tpp80) cc_final: 0.7336 (tpp80)
REVERT: A  358 TYR cc_start: 0.8066 (m-80) cc_final: 0.7756 (m-80)
REVERT: B   63 TRP cc_start: 0.7487 (m-10) cc_final: 0.6781 (m-10)
REVERT: R   56 CYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7073 (m)
REVERT: R  139 TYR cc_start: 0.8205 (t80) cc_final: 0.7840 (t80)
REVERT: R  179 ASP cc_start: 0.7019 (p0) cc_final: 0.6389 (t70)
REVERT: R  204 MET cc_start: 0.7385 (ttm) cc_final: 0.7163 (mtp)
  outliers start: 23
  outliers final: 21
  residues processed: 141
  average time/residue: 0.5517
  time to fit residues: 101.8253
Evaluate side-chains
  146 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 CYS
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain R residue   56 CYS
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  191 SER
Chi-restraints excluded: chain R residue  281 LEU
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  306 LYS
Chi-restraints excluded: chain R residue  309 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 32 optimal weight:    0.1980
   chunk 7 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.4204 r_free = 0.4204 target = 0.182919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.147669 restraints weight = 24347.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.3853 rms_B_bonded: 2.97
r_work: 0.3710 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3710
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3710 r_free = 0.3710    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3710 r_free = 0.3710    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3710
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7100  Z= 0.136
  Angle     :  0.528   9.923   9618  Z= 0.284
  Chirality :  0.041   0.437   1104
  Planarity :  0.004   0.063   1219
  Dihedral  :  4.997  45.830    992
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 22.28 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.29), residues: 875
  helix:  2.26 (0.27), residues: 367
  sheet: -1.74 (0.41), residues: 161
  loop : -1.23 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 281 
 HIS   0.003   0.001   HIS R 223 
 PHE   0.016   0.001   PHE A 290 
 TYR   0.012   0.001   TYR A 311 
 ARG   0.009   0.001   ARG R 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04006 (  363)
  hydrogen bonds       : angle       4.47695 ( 1053)
  SS BOND              : bond        0.00923 (    1)
  SS BOND              : angle       1.81634 (    2)
  covalent geometry    : bond        0.00297 ( 7099)
  covalent geometry    : angle       0.52770 ( 9616)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  151 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 1.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.7931 (mt0) cc_final: 0.7704 (mt0)
REVERT: A  280 LYS cc_start: 0.8126 (ttpp) cc_final: 0.7893 (tptt)
REVERT: A  358 TYR cc_start: 0.8046 (m-80) cc_final: 0.7737 (m-80)
REVERT: B   63 TRP cc_start: 0.7458 (m-10) cc_final: 0.6721 (m-10)
REVERT: B  258 ASP cc_start: 0.7223 (t70) cc_final: 0.6650 (t0)
REVERT: R   56 CYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7056 (m)
REVERT: R  147 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7254 (tp30)
REVERT: R  179 ASP cc_start: 0.7072 (p0) cc_final: 0.6463 (t70)
REVERT: R  204 MET cc_start: 0.7386 (ttm) cc_final: 0.7174 (mtp)
  outliers start: 22
  outliers final: 20
  residues processed: 142
  average time/residue: 0.6440
  time to fit residues: 120.4980
Evaluate side-chains
  147 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 CYS
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain R residue   56 CYS
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  191 SER
Chi-restraints excluded: chain R residue  281 LEU
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  306 LYS
Chi-restraints excluded: chain R residue  309 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   chunk 83 optimal weight:    0.0470
   chunk 1 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 54 optimal weight:    0.2980
   chunk 45 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.6278

-------------------------------------------------------------------------------
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 = 0.4232 r_free = 0.4232 target = 0.185913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.150534 restraints weight = 24422.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3878 rms_B_bonded: 2.99
r_work: 0.3739 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3740
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3740 r_free = 0.3740    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3740 r_free = 0.3740    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3740
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7100  Z= 0.108
  Angle     :  0.501   9.968   9618  Z= 0.268
  Chirality :  0.040   0.441   1104
  Planarity :  0.004   0.063   1219
  Dihedral  :  4.695  45.685    992
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 22.95 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.30), residues: 875
  helix:  2.55 (0.27), residues: 366
  sheet: -1.62 (0.42), residues: 161
  loop : -1.08 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 281 
 HIS   0.002   0.001   HIS B 311 
 PHE   0.013   0.001   PHE A 290 
 TYR   0.011   0.001   TYR A 311 
 ARG   0.009   0.000   ARG R 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03684 (  363)
  hydrogen bonds       : angle       4.30376 ( 1053)
  SS BOND              : bond        0.00934 (    1)
  SS BOND              : angle       1.48290 (    2)
  covalent geometry    : bond        0.00233 ( 7099)
  covalent geometry    : angle       0.50033 ( 9616)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  150 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 LYS cc_start: 0.8108 (ttpp) cc_final: 0.7864 (tptt)
REVERT: A  358 TYR cc_start: 0.8024 (m-80) cc_final: 0.7701 (m-80)
REVERT: B   63 TRP cc_start: 0.7440 (m-10) cc_final: 0.6706 (m-10)
REVERT: B  258 ASP cc_start: 0.7144 (t70) cc_final: 0.6598 (t0)
REVERT: R   56 CYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7055 (m)
REVERT: R  139 TYR cc_start: 0.8208 (t80) cc_final: 0.7831 (t80)
REVERT: R  179 ASP cc_start: 0.7109 (p0) cc_final: 0.6523 (t70)
  outliers start: 17
  outliers final: 15
  residues processed: 144
  average time/residue: 0.4913
  time to fit residues: 91.5056
Evaluate side-chains
  143 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 127
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 CYS
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain R residue   56 CYS
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  281 LEU
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  306 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 52 optimal weight:    0.3980
   chunk 18 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4214 r_free = 0.4214 target = 0.184105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.149345 restraints weight = 24388.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3878 rms_B_bonded: 2.94
r_work: 0.3737 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3734
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3734 r_free = 0.3734    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3734 r_free = 0.3734    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3734
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.2740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7100  Z= 0.119
  Angle     :  0.517  10.022   9618  Z= 0.276
  Chirality :  0.041   0.440   1104
  Planarity :  0.004   0.080   1219
  Dihedral  :  4.743  45.500    992
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 23.22 %
    Favored  : 74.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.30), residues: 875
  helix:  2.53 (0.27), residues: 368
  sheet: -1.53 (0.43), residues: 159
  loop : -1.13 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 281 
 HIS   0.002   0.001   HIS R 223 
 PHE   0.015   0.001   PHE A 290 
 TYR   0.011   0.001   TYR A 311 
 ARG   0.011   0.001   ARG R 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03736 (  363)
  hydrogen bonds       : angle       4.29854 ( 1053)
  SS BOND              : bond        0.01652 (    1)
  SS BOND              : angle       1.85350 (    2)
  covalent geometry    : bond        0.00260 ( 7099)
  covalent geometry    : angle       0.51642 ( 9616)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   58 is missing expected H atoms. Skipping.
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  144 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 1.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 LYS cc_start: 0.8099 (ttpp) cc_final: 0.7837 (tptt)
REVERT: A  358 TYR cc_start: 0.8041 (m-80) cc_final: 0.7707 (m-80)
REVERT: B   63 TRP cc_start: 0.7429 (m-10) cc_final: 0.6696 (m-10)
REVERT: B  258 ASP cc_start: 0.7142 (t70) cc_final: 0.6542 (t0)
REVERT: R   56 CYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7027 (m)
REVERT: R  139 TYR cc_start: 0.8215 (t80) cc_final: 0.7862 (t80)
REVERT: R  179 ASP cc_start: 0.7132 (p0) cc_final: 0.6458 (t70)
  outliers start: 16
  outliers final: 14
  residues processed: 138
  average time/residue: 0.5477
  time to fit residues: 98.0706
Evaluate side-chains
  142 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 CYS
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain R residue   56 CYS
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  281 LEU
Chi-restraints excluded: chain R residue  284 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 41 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 72 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0370
   chunk 74 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.6258

-------------------------------------------------------------------------------
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 = 0.4238 r_free = 0.4238 target = 0.186625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.151887 restraints weight = 24201.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3888 rms_B_bonded: 2.94
r_work: 0.3753 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3754
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3754 r_free = 0.3754    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3754 r_free = 0.3754    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3754
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.2762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7100  Z= 0.106
  Angle     :  0.501  10.060   9618  Z= 0.267
  Chirality :  0.040   0.443   1104
  Planarity :  0.005   0.080   1219
  Dihedral  :  4.622  47.937    992
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 23.22 %
    Favored  : 74.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.30), residues: 875
  helix:  2.68 (0.27), residues: 368
  sheet: -1.47 (0.43), residues: 159
  loop : -1.06 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 281 
 HIS   0.002   0.001   HIS B 311 
 PHE   0.014   0.001   PHE A 290 
 TYR   0.011   0.001   TYR A 311 
 ARG   0.011   0.001   ARG R 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03596 (  363)
  hydrogen bonds       : angle       4.21478 ( 1053)
  SS BOND              : bond        0.01543 (    1)
  SS BOND              : angle       1.41756 (    2)
  covalent geometry    : bond        0.00228 ( 7099)
  covalent geometry    : angle       0.50093 ( 9616)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7611.99 seconds
wall clock time: 134 minutes 2.54 seconds (8042.54 seconds total)