Starting phenix.real_space_refine
on Wed Mar 12 09:59:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p3r_13185/03_2025/7p3r_13185.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p3r_13185/03_2025/7p3r_13185.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p3r_13185/03_2025/7p3r_13185.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p3r_13185/03_2025/7p3r_13185.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p3r_13185/03_2025/7p3r_13185.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p3r_13185/03_2025/7p3r_13185.cif"
  }
  resolution = 3.65
  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=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       8      5.16       5
     C    4702      2.51       5
     N    1454      2.21       5
     O    1574      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7738
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 1902
          Classifications: {'peptide': 328}
          Incomplete info: {'truncation_to_alanine': 175}
          Link IDs: {'PTRANS': 6, 'TRANS': 321}
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 557
          Unresolved non-hydrogen angles: 722
          Unresolved non-hydrogen dihedrals: 456
          Unresolved non-hydrogen chiralities: 63
          Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 1, 'ASN:plan1': 9, 'TRP:plan': 5, 'ASP:plan': 19, 'PHE:plan': 7, 'GLU:plan': 9, 'HIS:plan': 3}
          Unresolved non-hydrogen planarities: 273
    Chain: "B"
      Number of atoms: 1967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 1967
          Classifications: {'peptide': 341}
          Incomplete info: {'truncation_to_alanine': 186}
          Link IDs: {'PTRANS': 6, 'TRANS': 334}
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 590
          Unresolved non-hydrogen angles: 764
          Unresolved non-hydrogen dihedrals: 481
          Unresolved non-hydrogen chiralities: 67
          Planarities with less than four sites: {'GLN:plan1': 15, 'TYR:plan': 1, 'ASN:plan1': 9, 'TRP:plan': 5, 'ASP:plan': 19, 'PHE:plan': 7, 'GLU:plan': 9, 'HIS:plan': 3}
          Unresolved non-hydrogen planarities: 289
    Chain: "C"
      Number of atoms: 1902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 1902
          Classifications: {'peptide': 328}
          Incomplete info: {'truncation_to_alanine': 175}
          Link IDs: {'PTRANS': 6, 'TRANS': 321}
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 557
          Unresolved non-hydrogen angles: 722
          Unresolved non-hydrogen dihedrals: 456
          Unresolved non-hydrogen chiralities: 63
          Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 1, 'ASN:plan1': 9, 'TRP:plan': 5, 'ASP:plan': 19, 'PHE:plan': 7, 'GLU:plan': 9, 'HIS:plan': 3}
          Unresolved non-hydrogen planarities: 273
    Chain: "D"
      Number of atoms: 1967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 1967
          Classifications: {'peptide': 341}
          Incomplete info: {'truncation_to_alanine': 186}
          Link IDs: {'PTRANS': 6, 'TRANS': 334}
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 590
          Unresolved non-hydrogen angles: 764
          Unresolved non-hydrogen dihedrals: 481
          Unresolved non-hydrogen chiralities: 67
          Planarities with less than four sites: {'GLN:plan1': 15, 'TYR:plan': 1, 'ASN:plan1': 9, 'TRP:plan': 5, 'ASP:plan': 19, 'PHE:plan': 7, 'GLU:plan': 9, 'HIS:plan': 3}
          Unresolved non-hydrogen planarities: 289
  Time building chain proxies: 7.51, per 1000 atoms: 0.97
  Number of scatterers: 7738
  At special positions: 0
  Unit cell: (157.342, 128.166, 110.452, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       8     16.00
     O    1574      8.00
     N    1454      7.00
     C    4702      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.15
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2524

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 0 sheets defined
      89.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 35
      removed outlier: 3.964A  pdb=" N   ILE A  25 " --> pdb=" O   ALA A  21 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   THR A  35 " --> pdb=" O   ALA A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 52
    Processing helix  chain 'A' and resid 56 through 66
      removed outlier: 4.185A  pdb=" N   LYS A  62 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 75
    Processing helix  chain 'A' and resid 76 through 81
      removed outlier: 3.532A  pdb=" N   ILE A  81 " --> pdb=" O   PRO A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 101
      removed outlier: 3.675A  pdb=" N   ALA A  89 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ILE A  94 " --> pdb=" O   SER A  90 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ASP A 101 " --> pdb=" O   LEU A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 158
      removed outlier: 4.124A  pdb=" N   ILE A 118 " --> pdb=" O   GLN A 114 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   SER A 127 " --> pdb=" O   SER A 123 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   GLY A 128 " --> pdb=" O   SER A 124 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   ILE A 129 " --> pdb=" O   GLN A 125 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LYS A 138 " --> pdb=" O   LYS A 134 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   TRP A 143 " --> pdb=" O   GLU A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 217
      removed outlier: 3.904A  pdb=" N   TYR A 195 " --> pdb=" O   LYS A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 315
      removed outlier: 3.863A  pdb=" N   SER A 293 " --> pdb=" O   GLU A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 345
      removed outlier: 4.382A  pdb=" N   ILE A 326 " --> pdb=" O   MET A 322 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   LYS A 329 " --> pdb=" O   ILE A 325 " (cutoff:3.500A)
      removed outlier: 5.489A  pdb=" N   VAL A 330 " --> pdb=" O   ILE A 326 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ASP A 341 " --> pdb=" O   ASN A 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 35
      removed outlier: 3.694A  pdb=" N   THR B  15 " --> pdb=" O   THR B  11 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   SER B  17 " --> pdb=" O   GLN B  13 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   THR B  22 " --> pdb=" O   ALA B  18 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ILE B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   HIS B  30 " --> pdb=" O   THR B  26 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   THR B  35 " --> pdb=" O   ALA B  31 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 63
      removed outlier: 3.663A  pdb=" N   ALA B  57 " --> pdb=" O   LYS B  53 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ALA B  61 " --> pdb=" O   ALA B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 72
      removed outlier: 3.656A  pdb=" N   GLN B  71 " --> pdb=" O   ASP B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 98
      removed outlier: 4.025A  pdb=" N   VAL B  80 " --> pdb=" O   ILE B  76 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   THR B  86 " --> pdb=" O   ASN B  82 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ALA B  89 " --> pdb=" O   ALA B  85 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   ILE B  91 " --> pdb=" O   PHE B  87 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   ASP B  92 " --> pdb=" O   GLN B  88 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU B  97 " --> pdb=" O   ALA B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 157
      removed outlier: 3.514A  pdb=" N   GLN B 113 " --> pdb=" O   ASN B 109 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   TRP B 143 " --> pdb=" O   GLU B 139 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   ASP B 153 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
      removed outlier: 5.105A  pdb=" N   LEU B 154 " --> pdb=" O   ALA B 150 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   VAL B 155 " --> pdb=" O   HIS B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 163 through 217
      removed outlier: 4.073A  pdb=" N   TYR B 195 " --> pdb=" O   LYS B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 319
      removed outlier: 3.560A  pdb=" N   ALA B 273 " --> pdb=" O   GLN B 269 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   THR B 290 " --> pdb=" O   SER B 286 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   TRP B 302 " --> pdb=" O   PHE B 298 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLY B 319 " --> pdb=" O   LYS B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 328
      removed outlier: 3.631A  pdb=" N   ILE B 326 " --> pdb=" O   MET B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 349
      removed outlier: 4.193A  pdb=" N   LYS B 336 " --> pdb=" O   SER B 332 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   GLU B 338 " --> pdb=" O   ALA B 334 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASP B 341 " --> pdb=" O   ASN B 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 35
    Processing helix  chain 'C' and resid 46 through 67
    Processing helix  chain 'C' and resid 67 through 85
      removed outlier: 3.965A  pdb=" N   ILE C  76 " --> pdb=" O   VAL C  72 " (cutoff:3.500A)
      Proline residue:  C  77  - end of helix
      removed outlier: 3.812A  pdb=" N   ASN C  82 " --> pdb=" O   SER C  78 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   PHE C  83 " --> pdb=" O   SER C  79 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA C  85 " --> pdb=" O   ILE C  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 101
      removed outlier: 3.577A  pdb=" N   TYR C  98 " --> pdb=" O   ILE C  94 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 109 through 126
      removed outlier: 3.784A  pdb=" N   SER C 124 " --> pdb=" O   THR C 120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 126 through 216
      removed outlier: 3.981A  pdb=" N   ASN C 137 " --> pdb=" O   VAL C 133 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   LYS C 138 " --> pdb=" O   LYS C 134 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   TRP C 143 " --> pdb=" O   GLU C 139 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ASP C 152 " --> pdb=" O   GLN C 148 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ASP C 153 " --> pdb=" O   ALA C 149 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   LEU C 154 " --> pdb=" O   ALA C 150 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   ASN C 160 " --> pdb=" O   ASN C 156 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ILE C 161 " --> pdb=" O   GLY C 157 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   GLN C 162 " --> pdb=" O   ALA C 158 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   VAL C 194 " --> pdb=" O   ASN C 190 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   TYR C 195 " --> pdb=" O   LYS C 191 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 223 through 316
      removed outlier: 4.102A  pdb=" N   ILE C 228 " --> pdb=" O   VAL C 224 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   ALA C 229 " --> pdb=" O   SER C 225 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ALA C 230 " --> pdb=" O   GLY C 226 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ILE C 272 " --> pdb=" O   GLN C 268 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ALA C 273 " --> pdb=" O   GLN C 269 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   SER C 296 " --> pdb=" O   THR C 292 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   THR C 301 " --> pdb=" O   ASP C 297 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL C 304 " --> pdb=" O   THR C 300 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   VAL C 312 " --> pdb=" O   GLU C 308 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   VAL C 313 " --> pdb=" O   LEU C 309 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 323 through 345
      removed outlier: 6.171A  pdb=" N   LYS C 329 " --> pdb=" O   ILE C 325 " (cutoff:3.500A)
      removed outlier: 5.295A  pdb=" N   VAL C 330 " --> pdb=" O   ILE C 326 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   VAL C 343 " --> pdb=" O   TRP C 339 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 12 through 35
      removed outlier: 3.580A  pdb=" N   VAL D  24 " --> pdb=" O   LEU D  20 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE D  25 " --> pdb=" O   ALA D  21 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR D  35 " --> pdb=" O   ALA D  31 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 46 through 67
      removed outlier: 4.152A  pdb=" N   LYS D  52 " --> pdb=" O   ASP D  48 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ALA D  57 " --> pdb=" O   LYS D  53 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   ALA D  61 " --> pdb=" O   ALA D  57 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   TRP D  64 " --> pdb=" O   VAL D  60 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ILE D  65 " --> pdb=" O   ALA D  61 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ASP D  67 " --> pdb=" O   GLN D  63 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 73
    Processing helix  chain 'D' and resid 75 through 84
      removed outlier: 3.890A  pdb=" N   SER D  79 " --> pdb=" O   SER D  75 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   VAL D  80 " --> pdb=" O   ILE D  76 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   ILE D  81 " --> pdb=" O   PRO D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 89 through 98
      removed outlier: 3.584A  pdb=" N   ALA D  93 " --> pdb=" O   ALA D  89 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ILE D  94 " --> pdb=" O   SER D  90 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLU D  96 " --> pdb=" O   ASP D  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 156
      removed outlier: 3.992A  pdb=" N   ASP D 153 " --> pdb=" O   ALA D 149 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   LEU D 154 " --> pdb=" O   ALA D 150 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 163 through 218
      removed outlier: 3.910A  pdb=" N   PHE D 205 " --> pdb=" O   GLY D 201 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ALA D 218 " --> pdb=" O   THR D 214 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 220 through 319
      removed outlier: 3.629A  pdb=" N   ALA D 287 " --> pdb=" O   ALA D 283 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   GLU D 289 " --> pdb=" O   VAL D 285 " (cutoff:3.500A)
      removed outlier: 4.944A  pdb=" N   THR D 290 " --> pdb=" O   SER D 286 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   VAL D 312 " --> pdb=" O   GLU D 308 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 322 through 328
      removed outlier: 3.936A  pdb=" N   ILE D 326 " --> pdb=" O   MET D 322 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 333 through 349
      removed outlier: 4.015A  pdb=" N   VAL D 343 " --> pdb=" O   TRP D 339 " (cutoff:3.500A)

    937 hydrogen bonds defined for protein.
    2811 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.42

  Time building geometry restraints manager: 2.53 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2589
        1.34 -     1.45: 578
        1.45 -     1.57: 4571
        1.57 -     1.68: 0
        1.68 -     1.80: 16
  Bond restraints: 7754
  Sorted by residual:
  bond pdb=" C   ILE C  76 "
       pdb=" N   PRO C  77 "
    ideal  model  delta    sigma   weight residual
    1.336  1.386 -0.050 1.25e-02 6.40e+03 1.60e+01
  bond pdb=" CB  THR C 242 "
       pdb=" CG2 THR C 242 "
    ideal  model  delta    sigma   weight residual
    1.521  1.436  0.085 3.30e-02 9.18e+02 6.69e+00
  bond pdb=" CB  ILE A 237 "
       pdb=" CG2 ILE A 237 "
    ideal  model  delta    sigma   weight residual
    1.521  1.445  0.076 3.30e-02 9.18e+02 5.30e+00
  bond pdb=" CB  ILE A 236 "
       pdb=" CG2 ILE A 236 "
    ideal  model  delta    sigma   weight residual
    1.521  1.449  0.072 3.30e-02 9.18e+02 4.77e+00
  bond pdb=" CB  VAL D 208 "
       pdb=" CG1 VAL D 208 "
    ideal  model  delta    sigma   weight residual
    1.521  1.461  0.060 3.30e-02 9.18e+02 3.35e+00
  ... (remaining 7749 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 10364
        1.99 -     3.97: 297
        3.97 -     5.96: 23
        5.96 -     7.94: 3
        7.94 -     9.93: 3
  Bond angle restraints: 10690
  Sorted by residual:
  angle pdb=" C   PHE B  37 "
        pdb=" N   THR B  38 "
        pdb=" CA  THR B  38 "
      ideal   model   delta    sigma   weight residual
     120.69  130.62   -9.93 2.95e+00 1.15e-01 1.13e+01
  angle pdb=" N   ILE A  76 "
        pdb=" CA  ILE A  76 "
        pdb=" C   ILE A  76 "
      ideal   model   delta    sigma   weight residual
     108.88  115.88   -7.00 2.16e+00 2.14e-01 1.05e+01
  angle pdb=" C   ASP A 252 "
        pdb=" N   ASP A 253 "
        pdb=" CA  ASP A 253 "
      ideal   model   delta    sigma   weight residual
     122.06  116.16    5.90 1.86e+00 2.89e-01 1.01e+01
  angle pdb=" N   ILE C  76 "
        pdb=" CA  ILE C  76 "
        pdb=" C   ILE C  76 "
      ideal   model   delta    sigma   weight residual
     108.88  115.72   -6.84 2.16e+00 2.14e-01 1.00e+01
  angle pdb=" N   VAL D 155 "
        pdb=" CA  VAL D 155 "
        pdb=" CB  VAL D 155 "
      ideal   model   delta    sigma   weight residual
     111.75  103.19    8.56 2.73e+00 1.34e-01 9.84e+00
  ... (remaining 10685 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.38: 4337
       17.38 -    34.76: 214
       34.76 -    52.14: 44
       52.14 -    69.52: 8
       69.52 -    86.90: 11
  Dihedral angle restraints: 4614
    sinusoidal: 748
      harmonic: 3866
  Sorted by residual:
  dihedral pdb=" CA  ASP D  84 "
           pdb=" C   ASP D  84 "
           pdb=" N   ALA D  85 "
           pdb=" CA  ALA D  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.20   23.80     0      5.00e+00 4.00e-02 2.27e+01
  dihedral pdb=" CA  LEU D  50 "
           pdb=" C   LEU D  50 "
           pdb=" N   SER D  51 "
           pdb=" CA  SER D  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.59   23.41     0      5.00e+00 4.00e-02 2.19e+01
  dihedral pdb=" CA  ASP D  67 "
           pdb=" C   ASP D  67 "
           pdb=" N   LEU D  68 "
           pdb=" CA  LEU D  68 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.65  -22.35     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 4611 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1124
       0.056 -    0.112: 247
       0.112 -    0.168: 38
       0.168 -    0.224: 7
       0.224 -    0.280: 2
  Chirality restraints: 1418
  Sorted by residual:
  chirality pdb=" CB  ILE A 236 "
            pdb=" CA  ILE A 236 "
            pdb=" CG1 ILE A 236 "
            pdb=" CG2 ILE A 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" CB  VAL D 208 "
            pdb=" CA  VAL D 208 "
            pdb=" CG1 VAL D 208 "
            pdb=" CG2 VAL D 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CB  ILE C 236 "
            pdb=" CA  ILE C 236 "
            pdb=" CG1 ILE C 236 "
            pdb=" CG2 ILE C 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 1415 not shown)

  Planarity restraints: 1486
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 237 "    0.012 2.00e-02 2.50e+03   2.35e-02 5.50e+00
        pdb=" C   ILE A 237 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   ILE A 237 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ALA A 238 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B  62 "   -0.012 2.00e-02 2.50e+03   2.33e-02 5.42e+00
        pdb=" C   LYS B  62 "    0.040 2.00e-02 2.50e+03
        pdb=" O   LYS B  62 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLN B  63 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 208 "   -0.011 2.00e-02 2.50e+03   2.24e-02 5.03e+00
        pdb=" C   VAL D 208 "    0.039 2.00e-02 2.50e+03
        pdb=" O   VAL D 208 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ALA D 209 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1483 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2591
        2.83 -     3.34: 7795
        3.34 -     3.86: 12977
        3.86 -     4.38: 13335
        4.38 -     4.90: 22463
  Nonbonded interactions: 59161
  Sorted by model distance:
  nonbonded pdb=" O   ALA D 221 "
            pdb=" OG  SER D 225 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   ALA B 238 "
            pdb=" OG1 THR B 242 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   GLY A 210 "
            pdb=" OG1 THR A 214 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OG1 THR B 214 "
            pdb=" OG  SER B 225 "
     model   vdw
     2.348 3.040
  nonbonded pdb=" O   TRP A  64 "
            pdb=" N   GLY A  69 "
     model   vdw
     2.351 3.120
  ... (remaining 59156 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 19 through 346)
  selection = chain 'C'
  selection = (chain 'D' and resid 19 through 346)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             18.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     25.560
  Find NCS groups from input model:        0.380
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6630
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      :  0.006   0.085   7754  Z= 0.393
  Angle     :  0.806   9.928  10690  Z= 0.508
  Chirality :  0.049   0.280   1418
  Planarity :  0.006   0.023   1486
  Dihedral  : 13.657  86.902   2090
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  9.55 %
    Favored  : 90.17 %
  Cbeta Deviations :  0.08 %
  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: -3.67 (0.17), residues: 1330
  helix: -2.13 (0.11), residues: 1151
  sheet:  None (None), residues: 0
  loop : -2.75 (0.38), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 243 
 PHE   0.007   0.001   PHE A 205 
 TYR   0.010   0.002   TYR C 254 
 ARG   0.003   0.001   ARG A 183 

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 1.055 
Fit side-chains
REVERT: A  163 LYS cc_start: 0.8008 (mttt) cc_final: 0.7742 (mtpt)
REVERT: A  187 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7375 (tm-30)
REVERT: A  248 ASN cc_start: 0.8239 (t0) cc_final: 0.7511 (m-40)
REVERT: B  171 ASP cc_start: 0.8350 (t70) cc_final: 0.8032 (t70)
REVERT: B  173 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7356 (tm-30)
REVERT: B  272 ILE cc_start: 0.8700 (pt) cc_final: 0.8498 (mm)
REVERT: C  160 ASN cc_start: 0.7470 (m-40) cc_final: 0.7260 (m-40)
REVERT: C  191 LYS cc_start: 0.8923 (tptt) cc_final: 0.8628 (tppt)
REVERT: D  251 ASP cc_start: 0.7231 (m-30) cc_final: 0.6820 (m-30)
REVERT: D  275 GLN cc_start: 0.6986 (tp40) cc_final: 0.6608 (mm110)
  outliers start: 1
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1717
  time to fit residues: 27.9701
Evaluate side-chains
  95 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    7.9990
   chunk 100 optimal weight:   30.0000
   chunk 55 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 67 optimal weight:   40.0000
   chunk 53 optimal weight:    3.9990
   chunk 103 optimal weight:   10.0000
   chunk 40 optimal weight:    0.5980
   chunk 62 optimal weight:   50.0000
   chunk 77 optimal weight:   50.0000
   chunk 119 optimal weight:    2.9990
   overall best weight:    3.7188

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

Flipped N/Q/H residues before XYZ refinement:
A 247 GLN
A 263 GLN
C 177 ASN
C 248 ASN
C 249 GLN
C 270 GLN
D 182 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.181062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.162892 restraints weight = 11464.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.163495 restraints weight = 23442.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.162469 restraints weight = 18551.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.4242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6311
moved from start:          0.1540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   7754  Z= 0.259
  Angle     :  0.478   5.256  10690  Z= 0.292
  Chirality :  0.038   0.148   1418
  Planarity :  0.003   0.016   1486
  Dihedral  :  4.748  21.920   1346
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 18.26 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.21), residues: 1330
  helix:  0.17 (0.14), residues: 1152
  sheet:  None (None), residues: 0
  loop : -2.17 (0.40), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 243 
 PHE   0.011   0.001   PHE A 205 
 TYR   0.009   0.001   TYR B 254 
 ARG   0.001   0.000   ARG A 183 

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 1.614 
Fit side-chains
   revert: symmetry clash
REVERT: A  248 ASN cc_start: 0.8219 (t0) cc_final: 0.7808 (m-40)
REVERT: B  272 ILE cc_start: 0.8555 (pt) cc_final: 0.8281 (mm)
REVERT: C  188 LYS cc_start: 0.8102 (tttt) cc_final: 0.7883 (ttmm)
REVERT: C  213 LEU cc_start: 0.8997 (tp) cc_final: 0.8778 (tp)
REVERT: D  175 MET cc_start: 0.7037 (mmt) cc_final: 0.6789 (mmt)
REVERT: D  191 LYS cc_start: 0.8427 (mptt) cc_final: 0.8183 (mppt)
REVERT: D  231 VAL cc_start: 0.9155 (p) cc_final: 0.8939 (t)
REVERT: D  251 ASP cc_start: 0.6964 (m-30) cc_final: 0.6682 (m-30)
  outliers start: 10
  outliers final: 7
  residues processed: 119
  average time/residue: 0.1953
  time to fit residues: 33.4090
Evaluate side-chains
  108 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  254 TYR
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  198 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 91 optimal weight:   10.0000
   chunk 113 optimal weight:    1.9990
   chunk 54 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   chunk 105 optimal weight:    3.9990
   chunk 65 optimal weight:   50.0000
   chunk 41 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9990
   chunk 38 optimal weight:   20.0000
   chunk 95 optimal weight:    1.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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 = 0.4425 r_free = 0.4425 target = 0.187320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.183006 restraints weight = 11770.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.182823 restraints weight = 21068.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.182504 restraints weight = 22303.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.4377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6101
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7754  Z= 0.214
  Angle     :  0.422   4.968  10690  Z= 0.254
  Chirality :  0.036   0.161   1418
  Planarity :  0.002   0.015   1486
  Dihedral  :  4.254  20.855   1346
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 18.54 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.22), residues: 1330
  helix:  1.30 (0.14), residues: 1157
  sheet:  None (None), residues: 0
  loop : -1.69 (0.44), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 243 
 PHE   0.008   0.001   PHE A 205 
 TYR   0.009   0.001   TYR D 254 
 ARG   0.002   0.001   ARG D 183 

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
REVERT: A  248 ASN cc_start: 0.8233 (t0) cc_final: 0.7718 (m-40)
REVERT: C  188 LYS cc_start: 0.8035 (tttt) cc_final: 0.7824 (ttmm)
REVERT: D  191 LYS cc_start: 0.8249 (mptt) cc_final: 0.8048 (mppt)
REVERT: D  231 VAL cc_start: 0.9222 (p) cc_final: 0.8972 (t)
  outliers start: 17
  outliers final: 10
  residues processed: 114
  average time/residue: 0.2146
  time to fit residues: 35.3108
Evaluate side-chains
  112 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 1.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  254 TYR
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain C residue  170 THR
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  206 MET
Chi-restraints excluded: chain D residue  248 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 116 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 97 optimal weight:   50.0000
   chunk 90 optimal weight:    1.9990
   chunk 95 optimal weight:   50.0000
   chunk 36 optimal weight:    6.9990
   chunk 71 optimal weight:    7.9990
   chunk 7 optimal weight:   80.0000
   chunk 78 optimal weight:    6.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
C 182 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.184091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.179671 restraints weight = 11711.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.179358 restraints weight = 22414.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.178994 restraints weight = 24062.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.4338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6178
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7754  Z= 0.283
  Angle     :  0.470   6.154  10690  Z= 0.278
  Chirality :  0.038   0.170   1418
  Planarity :  0.002   0.015   1486
  Dihedral  :  4.321  22.733   1346
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 23.31 %
    Favored  : 71.63 %
  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:  1.90 (0.22), residues: 1330
  helix:  1.68 (0.15), residues: 1154
  sheet:  None (None), residues: 0
  loop : -1.47 (0.44), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 243 
 PHE   0.014   0.001   PHE B 205 
 TYR   0.010   0.001   TYR D 254 
 ARG   0.002   0.001   ARG D 183 

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
REVERT: C  188 LYS cc_start: 0.8073 (tttt) cc_final: 0.7872 (ttmm)
REVERT: D  251 ASP cc_start: 0.6753 (m-30) cc_final: 0.6454 (m-30)
  outliers start: 18
  outliers final: 11
  residues processed: 109
  average time/residue: 0.1661
  time to fit residues: 26.0906
Evaluate side-chains
  108 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  254 TYR
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  206 MET
Chi-restraints excluded: chain D residue  224 VAL
Chi-restraints excluded: chain D residue  248 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 31 optimal weight:   60.0000
   chunk 57 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9980
   chunk 98 optimal weight:   60.0000
   chunk 67 optimal weight:   50.0000
   chunk 116 optimal weight:    3.9990
   chunk 91 optimal weight:    9.9990
   chunk 101 optimal weight:    0.0060
   chunk 120 optimal weight:    0.9990
   chunk 106 optimal weight:    6.9990
   chunk 114 optimal weight:    5.9990
   overall best weight:    1.3800

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

Flipped N/Q/H residues before XYZ refinement:
B 182 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.180703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.166652 restraints weight = 11496.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.165863 restraints weight = 19022.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.165385 restraints weight = 19492.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.4267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6295
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   0.035   7754  Z= 0.145
  Angle     :  0.391   4.887  10690  Z= 0.235
  Chirality :  0.035   0.153   1418
  Planarity :  0.002   0.014   1486
  Dihedral  :  3.861  18.102   1346
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 27.81 %
    Favored  : 69.66 %
  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:  2.90 (0.22), residues: 1330
  helix:  2.36 (0.14), residues: 1163
  sheet:  None (None), residues: 0
  loop : -1.42 (0.46), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 243 
 PHE   0.006   0.001   PHE A 205 
 TYR   0.009   0.001   TYR D 254 
 ARG   0.002   0.000   ARG C 183 

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
REVERT: A  248 ASN cc_start: 0.8064 (t0) cc_final: 0.7531 (m-40)
REVERT: D  191 LYS cc_start: 0.8423 (mppt) cc_final: 0.8177 (mppt)
  outliers start: 9
  outliers final: 8
  residues processed: 113
  average time/residue: 0.1825
  time to fit residues: 29.1599
Evaluate side-chains
  109 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  254 TYR
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain C residue  170 THR
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  206 MET
Chi-restraints excluded: chain D residue  224 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 29 optimal weight:   30.0000
   chunk 110 optimal weight:    7.9990
   chunk 128 optimal weight:   40.0000
   chunk 35 optimal weight:   20.0000
   chunk 5 optimal weight:    6.9990
   chunk 71 optimal weight:    8.9990
   chunk 91 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 41 optimal weight:   30.0000
   chunk 32 optimal weight:   50.0000
   chunk 61 optimal weight:   50.0000
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 247 GLN
D 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.181816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.177504 restraints weight = 11704.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.177199 restraints weight = 24394.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.176706 restraints weight = 27593.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.4320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6220
moved from start:          0.3059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   7754  Z= 0.364
  Angle     :  0.505   7.142  10690  Z= 0.298
  Chirality :  0.040   0.176   1418
  Planarity :  0.002   0.016   1486
  Dihedral  :  4.302  24.638   1346
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 25.84 %
    Favored  : 69.10 %
  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:  2.39 (0.22), residues: 1330
  helix:  2.00 (0.14), residues: 1162
  sheet:  None (None), residues: 0
  loop : -1.37 (0.46), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 243 
 PHE   0.011   0.001   PHE A 205 
 TYR   0.010   0.002   TYR D 254 
 ARG   0.001   0.000   ARG D 183 

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
REVERT: D  175 MET cc_start: 0.6874 (mmt) cc_final: 0.6589 (mmt)
REVERT: D  251 ASP cc_start: 0.6835 (m-30) cc_final: 0.6528 (m-30)
  outliers start: 18
  outliers final: 13
  residues processed: 107
  average time/residue: 0.2655
  time to fit residues: 41.4910
Evaluate side-chains
  105 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  254 TYR
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain C residue  170 THR
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  206 MET
Chi-restraints excluded: chain D residue  224 VAL
Chi-restraints excluded: chain D residue  248 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 91 optimal weight:    5.9990
   chunk 63 optimal weight:   40.0000
   chunk 94 optimal weight:    6.9990
   chunk 4 optimal weight:   50.0000
   chunk 97 optimal weight:   50.0000
   chunk 82 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 29 optimal weight:   30.0000
   chunk 86 optimal weight:    8.9990
   chunk 118 optimal weight:    0.9990
   chunk 101 optimal weight:   10.0000
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.4389 r_free = 0.4389 target = 0.183351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.178951 restraints weight = 11673.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.178664 restraints weight = 23158.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.178393 restraints weight = 24436.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.4339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6183
moved from start:          0.3269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7754  Z= 0.253
  Angle     :  0.451   5.646  10690  Z= 0.267
  Chirality :  0.037   0.158   1418
  Planarity :  0.002   0.015   1486
  Dihedral  :  4.089  19.063   1346
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 26.69 %
    Favored  : 68.82 %
  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:  2.79 (0.22), residues: 1330
  helix:  2.26 (0.14), residues: 1163
  sheet:  None (None), residues: 0
  loop : -1.29 (0.47), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 243 
 PHE   0.009   0.001   PHE A 205 
 TYR   0.008   0.001   TYR D 254 
 ARG   0.002   0.001   ARG D 183 

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
REVERT: B  175 MET cc_start: 0.8050 (mmt) cc_final: 0.7723 (mmt)
REVERT: B  191 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7972 (mmtp)
REVERT: D  175 MET cc_start: 0.6814 (mmt) cc_final: 0.6524 (mmt)
  outliers start: 16
  outliers final: 11
  residues processed: 102
  average time/residue: 0.1911
  time to fit residues: 28.7089
Evaluate side-chains
  99 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  254 TYR
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain C residue  170 THR
Chi-restraints excluded: chain C residue  202 VAL
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  206 MET
Chi-restraints excluded: chain D residue  224 VAL
Chi-restraints excluded: chain D residue  245 VAL
Chi-restraints excluded: chain D residue  248 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 99 optimal weight:    5.9990
   chunk 117 optimal weight:    0.9990
   chunk 78 optimal weight:    9.9990
   chunk 105 optimal weight:   60.0000
   chunk 61 optimal weight:   10.0000
   chunk 119 optimal weight:    5.9990
   chunk 44 optimal weight:   30.0000
   chunk 50 optimal weight:    0.9990
   chunk 60 optimal weight:    7.9990
   chunk 98 optimal weight:    6.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.4381 r_free = 0.4381 target = 0.182563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.178267 restraints weight = 11714.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.178187 restraints weight = 24248.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.178063 restraints weight = 20793.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.4336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6189
moved from start:          0.3517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7754  Z= 0.262
  Angle     :  0.463   6.237  10690  Z= 0.273
  Chirality :  0.037   0.162   1418
  Planarity :  0.002   0.015   1486
  Dihedral  :  4.109  23.357   1346
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 26.40 %
    Favored  : 68.82 %
  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:  2.92 (0.22), residues: 1330
  helix:  2.35 (0.14), residues: 1163
  sheet:  None (None), residues: 0
  loop : -1.21 (0.48), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 243 
 PHE   0.009   0.001   PHE A 205 
 TYR   0.010   0.001   TYR D 254 
 ARG   0.002   0.001   ARG D 183 

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
REVERT: D  269 GLN cc_start: 0.6769 (tm-30) cc_final: 0.6463 (tm-30)
  outliers start: 17
  outliers final: 14
  residues processed: 107
  average time/residue: 0.1560
  time to fit residues: 24.0456
Evaluate side-chains
  109 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  254 TYR
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  269 GLN
Chi-restraints excluded: chain C residue  170 THR
Chi-restraints excluded: chain C residue  202 VAL
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  206 MET
Chi-restraints excluded: chain D residue  224 VAL
Chi-restraints excluded: chain D residue  245 VAL
Chi-restraints excluded: chain D residue  248 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 60 optimal weight:   50.0000
   chunk 26 optimal weight:   20.0000
   chunk 50 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9980
   chunk 108 optimal weight:    8.9990
   chunk 4 optimal weight:   50.0000
   chunk 3 optimal weight:    5.9990
   chunk 96 optimal weight:   50.0000
   chunk 38 optimal weight:   20.0000
   chunk 59 optimal weight:   30.0000
   chunk 67 optimal weight:   50.0000
   overall best weight:    7.3990

-------------------------------------------------------------------------------
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 = 0.4350 r_free = 0.4350 target = 0.179318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.175106 restraints weight = 11972.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.175009 restraints weight = 25454.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.174691 restraints weight = 25500.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.4302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6266
moved from start:          0.3859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.079   7754  Z= 0.428
  Angle     :  0.567   9.591  10690  Z= 0.332
  Chirality :  0.042   0.186   1418
  Planarity :  0.003   0.019   1486
  Dihedral  :  4.654  24.562   1346
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 27.25 %
    Favored  : 67.70 %
  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:  1.98 (0.22), residues: 1330
  helix:  1.72 (0.14), residues: 1161
  sheet:  None (None), residues: 0
  loop : -1.46 (0.47), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 243 
 PHE   0.013   0.001   PHE A 205 
 TYR   0.011   0.002   TYR B 254 
 ARG   0.004   0.001   ARG D 183 

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
REVERT: D  251 ASP cc_start: 0.6863 (m-30) cc_final: 0.6576 (m-30)
REVERT: D  269 GLN cc_start: 0.6960 (tm-30) cc_final: 0.6632 (tm-30)
  outliers start: 18
  outliers final: 14
  residues processed: 110
  average time/residue: 0.1614
  time to fit residues: 25.8473
Evaluate side-chains
  108 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  254 TYR
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain C residue  170 THR
Chi-restraints excluded: chain C residue  202 VAL
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  206 MET
Chi-restraints excluded: chain D residue  224 VAL
Chi-restraints excluded: chain D residue  245 VAL
Chi-restraints excluded: chain D residue  248 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 122 optimal weight:    8.9990
   chunk 46 optimal weight:   50.0000
   chunk 57 optimal weight:    7.9990
   chunk 65 optimal weight:   50.0000
   chunk 31 optimal weight:    6.9990
   chunk 29 optimal weight:   40.0000
   chunk 86 optimal weight:   10.0000
   chunk 100 optimal weight:    4.9990
   chunk 7 optimal weight:   20.0000
   chunk 70 optimal weight:   50.0000
   chunk 51 optimal weight:    2.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 248 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.179901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.175616 restraints weight = 11868.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.175176 restraints weight = 24633.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.174727 restraints weight = 27860.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.4302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6265
moved from start:          0.4023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070   7754  Z= 0.375
  Angle     :  0.541   8.118  10690  Z= 0.314
  Chirality :  0.040   0.178   1418
  Planarity :  0.002   0.017   1486
  Dihedral  :  4.573  24.583   1346
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 28.93 %
    Favored  : 66.29 %
  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:  2.07 (0.22), residues: 1330
  helix:  1.79 (0.14), residues: 1160
  sheet:  None (None), residues: 0
  loop : -1.51 (0.49), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 243 
 PHE   0.009   0.001   PHE A 205 
 TYR   0.009   0.002   TYR D 254 
 ARG   0.002   0.001   ARG D 183 

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
  outliers start: 17
  outliers final: 14
  residues processed: 103
  average time/residue: 0.1611
  time to fit residues: 24.1097
Evaluate side-chains
  105 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 TYR
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain C residue  170 THR
Chi-restraints excluded: chain C residue  202 VAL
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  206 MET
Chi-restraints excluded: chain D residue  224 VAL
Chi-restraints excluded: chain D residue  245 VAL
Chi-restraints excluded: chain D residue  248 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 6 optimal weight:   50.0000
   chunk 100 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   chunk 33 optimal weight:   30.0000
   chunk 40 optimal weight:   40.0000
   chunk 5 optimal weight:    0.9990
   chunk 106 optimal weight:    0.7980
   chunk 81 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    2.1586

-------------------------------------------------------------------------------
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 = 0.4396 r_free = 0.4396 target = 0.183796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.179512 restraints weight = 11658.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.179319 restraints weight = 18019.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.179101 restraints weight = 20779.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.4348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6166
moved from start:          0.4067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7754  Z= 0.179
  Angle     :  0.434   6.271  10690  Z= 0.254
  Chirality :  0.036   0.167   1418
  Planarity :  0.002   0.015   1486
  Dihedral  :  3.981  19.049   1346
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 31.18 %
    Favored  : 66.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.23 (0.23), residues: 1330
  helix:  2.57 (0.14), residues: 1166
  sheet:  None (None), residues: 0
  loop : -1.28 (0.51), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 243 
 PHE   0.005   0.001   PHE A 205 
 TYR   0.008   0.001   TYR D 254 
 ARG   0.002   0.000   ARG C 183 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3055.82 seconds
wall clock time: 55 minutes 43.96 seconds (3343.96 seconds total)