Starting phenix.real_space_refine
on Wed Feb 12 20:55:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rmh_24570/02_2025/7rmh_24570.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rmh_24570/02_2025/7rmh_24570.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rmh_24570/02_2025/7rmh_24570.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rmh_24570/02_2025/7rmh_24570.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rmh_24570/02_2025/7rmh_24570.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rmh_24570/02_2025/7rmh_24570.cif"
  }
  resolution = 3.1
  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=  -0.002 sd=   0.314
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1082 atoms to isotropic.
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      55      5.16       5
     C    4811      2.51       5
     N    1267      2.21       5
     O    1301      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7434
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1665
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 5, 'TRANS': 210}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 153
          Unresolved non-hydrogen angles: 184
          Unresolved non-hydrogen dihedrals: 122
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 9}
          Unresolved non-hydrogen planarities: 99
    Chain: "B"
      Number of atoms: 2319
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 322, 2319
          Classifications: {'peptide': 322}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 5, 'TRANS': 316}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 149
          Unresolved non-hydrogen angles: 183
          Unresolved non-hydrogen dihedrals: 115
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 5, 'ASP:plan': 13}
          Unresolved non-hydrogen planarities: 113
    Chain: "G"
      Number of atoms: 245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 245
          Classifications: {'peptide': 38}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 1, 'TRANS': 36}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 28
    Chain: "N"
      Number of atoms: 851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 851
          Classifications: {'peptide': 115}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "R"
      Number of atoms: 2269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2269
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 13, 'TRANS': 270}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 72
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 31
    Chain: "S"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 84
          Classifications: {'peptide': 11}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 8}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "S"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.14, per 1000 atoms: 0.69
  Number of scatterers: 7434
  At special positions: 0
  Unit cell: (75.68, 98.9, 131.58, 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      55     16.00
     O    1301      8.00
     N    1267      7.00
     C    4811      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 105 " - pdb=" SG  CYS R 180 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.69
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1876

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 11 sheets defined
      40.8% alpha, 22.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 38
      removed outlier: 3.987A  pdb=" N   ALA A  18 " --> pdb=" O   ASN A  14 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLN A  19 " --> pdb=" O   GLU A  15 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LYS A  25 " --> pdb=" O   GLU A  21 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ARG A  38 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
      removed outlier: 3.568A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   VAL A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LYS A  58 " --> pdb=" O   SER A  54 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   GLN A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   MET A  60 " --> pdb=" O   ILE A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 238
      removed outlier: 3.660A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE A 238 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 294 through 303
      removed outlier: 3.659A  pdb=" N   ALA A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 351
      removed outlier: 4.214A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 4.073A  pdb=" N   ARG A 389 " --> pdb=" O   ARG A 385 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLN A 390 " --> pdb=" O   MET A 386 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   TYR A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 25
    Processing helix  chain 'B' and resid 30 through 34
    Processing helix  chain 'G' and resid 14 through 23
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.608A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.705A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.733A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 28 through 32'
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.759A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 28 through 60
      removed outlier: 3.748A  pdb=" N   ILE R  32 " --> pdb=" O   PRO R  28 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ILE R  42 " --> pdb=" O   ALA R  38 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   HIS R  60 " --> pdb=" O   ILE R  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 65 through 67
      No H-bonds generated for 'chain 'R' and resid 65 through 67'
    Processing helix  chain 'R' and resid 68 through 85
      removed outlier: 3.623A  pdb=" N   PHE R  84 " --> pdb=" O   SER R  80 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 86 through 94
    Processing helix  chain 'R' and resid 101 through 135
      Proline residue:  R 112  - end of helix
    Processing helix  chain 'R' and resid 143 through 168
      Proline residue:  R 164  - end of helix
      removed outlier: 3.564A  pdb=" N   TYR R 168 " --> pdb=" O   PRO R 164 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 191 through 205
    Processing helix  chain 'R' and resid 205 through 224
    Processing helix  chain 'R' and resid 240 through 270
      Proline residue:  R 263  - end of helix
    Processing helix  chain 'R' and resid 271 through 273
      No H-bonds generated for 'chain 'R' and resid 271 through 273'
    Processing helix  chain 'R' and resid 274 through 279
      removed outlier: 3.817A  pdb=" N   LEU R 277 " --> pdb=" O   ASN R 274 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   TYR R 278 " --> pdb=" O   PRO R 275 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   LEU R 279 " --> pdb=" O   ASP R 276 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 274 through 279'
    Processing helix  chain 'R' and resid 280 through 296
      removed outlier: 4.103A  pdb=" N   GLN R 284 " --> pdb=" O   LYS R 280 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 299 through 309
      removed outlier: 3.953A  pdb=" N   ILE R 303 " --> pdb=" O   MET R 299 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ASN R 309 " --> pdb=" O   TYR R 305 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 309 through 320
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.238A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.872A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 8.226A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.119A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.123A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.063A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.190A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.165A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.890A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.378A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.818A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.035A  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: 3.911A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.303A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.773A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.923A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.596A  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: 3.785A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 5.496A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 169 through 174

    370 hydrogen bonds defined for protein.
    1059 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: 2.13

  Time building geometry restraints manager: 2.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2330
        1.34 -     1.46: 1967
        1.46 -     1.59: 3234
        1.59 -     1.71: 0
        1.71 -     1.83: 79
  Bond restraints: 7610
  Sorted by residual:
  bond pdb=" N   GLN R  24 "
       pdb=" CA  GLN R  24 "
    ideal  model  delta    sigma   weight residual
    1.456  1.496 -0.040 1.33e-02 5.65e+03 8.92e+00
  bond pdb=" C   ARG S   1 "
       pdb=" N   PRO S   2 "
    ideal  model  delta    sigma   weight residual
    1.334  1.383 -0.049 2.34e-02 1.83e+03 4.41e+00
  bond pdb=" CB  PRO R 208 "
       pdb=" CG  PRO R 208 "
    ideal  model  delta    sigma   weight residual
    1.492  1.403  0.089 5.00e-02 4.00e+02 3.18e+00
  bond pdb=" CA  LEU R 262 "
       pdb=" C   LEU R 262 "
    ideal  model  delta    sigma   weight residual
    1.521  1.539 -0.017 1.08e-02 8.57e+03 2.62e+00
  bond pdb=" C   PHE R 163 "
       pdb=" N   PRO R 164 "
    ideal  model  delta    sigma   weight residual
    1.336  1.355 -0.019 1.25e-02 6.40e+03 2.24e+00
  ... (remaining 7605 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 9989
        1.70 -     3.39: 323
        3.39 -     5.09: 44
        5.09 -     6.79: 14
        6.79 -     8.49: 9
  Bond angle restraints: 10379
  Sorted by residual:
  angle pdb=" N   PHE R 111 "
        pdb=" CA  PHE R 111 "
        pdb=" C   PHE R 111 "
      ideal   model   delta    sigma   weight residual
     109.81  118.30   -8.49 2.21e+00 2.05e-01 1.47e+01
  angle pdb=" N   LEU R 270 "
        pdb=" CA  LEU R 270 "
        pdb=" C   LEU R 270 "
      ideal   model   delta    sigma   weight residual
     112.75  116.95   -4.20 1.36e+00 5.41e-01 9.54e+00
  angle pdb=" CA  TRP B 169 "
        pdb=" CB  TRP B 169 "
        pdb=" CG  TRP B 169 "
      ideal   model   delta    sigma   weight residual
     113.60  119.05   -5.45 1.90e+00 2.77e-01 8.23e+00
  angle pdb=" N   ASN R 301 "
        pdb=" CA  ASN R 301 "
        pdb=" C   ASN R 301 "
      ideal   model   delta    sigma   weight residual
     109.81  115.85   -6.04 2.21e+00 2.05e-01 7.47e+00
  angle pdb=" CA  ARG R 141 "
        pdb=" CB  ARG R 141 "
        pdb=" CG  ARG R 141 "
      ideal   model   delta    sigma   weight residual
     114.10  119.53   -5.43 2.00e+00 2.50e-01 7.38e+00
  ... (remaining 10374 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.80: 3987
       16.80 -    33.61: 340
       33.61 -    50.41: 72
       50.41 -    67.22: 8
       67.22 -    84.02: 5
  Dihedral angle restraints: 4412
    sinusoidal: 1520
      harmonic: 2892
  Sorted by residual:
  dihedral pdb=" CA  CYS N  99 "
           pdb=" C   CYS N  99 "
           pdb=" N   PRO N 100 "
           pdb=" CA  PRO N 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.35  -26.65     0      5.00e+00 4.00e-02 2.84e+01
  dihedral pdb=" CA  VAL A 224 "
           pdb=" C   VAL A 224 "
           pdb=" N   GLY A 225 "
           pdb=" CA  GLY A 225 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.00   23.00     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.70  -22.30     0      5.00e+00 4.00e-02 1.99e+01
  ... (remaining 4409 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 806
       0.043 -    0.086: 295
       0.086 -    0.130: 86
       0.130 -    0.173: 20
       0.173 -    0.216: 3
  Chirality restraints: 1210
  Sorted by residual:
  chirality pdb=" CB  VAL R 200 "
            pdb=" CA  VAL R 200 "
            pdb=" CG1 VAL R 200 "
            pdb=" CG2 VAL R 200 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  PHE R 111 "
            pdb=" N   PHE R 111 "
            pdb=" C   PHE R 111 "
            pdb=" CB  PHE R 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.03e-01
  chirality pdb=" CG  LEU B 284 "
            pdb=" CB  LEU B 284 "
            pdb=" CD1 LEU B 284 "
            pdb=" CD2 LEU B 284 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 7.97e-01
  ... (remaining 1207 not shown)

  Planarity restraints: 1294
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET R 174 "    0.034 5.00e-02 4.00e+02   5.15e-02 4.24e+00
        pdb=" N   PRO R 175 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO R 175 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO R 175 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS N  87 "    0.033 5.00e-02 4.00e+02   5.04e-02 4.07e+00
        pdb=" N   PRO N  88 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO N  88 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO N  88 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 224 "   -0.009 2.00e-02 2.50e+03   1.82e-02 3.32e+00
        pdb=" C   VAL A 224 "    0.032 2.00e-02 2.50e+03
        pdb=" O   VAL A 224 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLY A 225 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1291 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2015
        2.81 -     3.33: 5941
        3.33 -     3.86: 11584
        3.86 -     4.38: 12745
        4.38 -     4.90: 23751
  Nonbonded interactions: 56036
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   ALA R  36 "
            pdb=" OG1 THR R  40 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" OE1 GLN N  39 "
            pdb=" OH  TYR N  95 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" O   LEU B 168 "
            pdb=" OG1 THR B 177 "
     model   vdw
     2.368 3.040
  nonbonded pdb=" NH1 ARG N  67 "
            pdb=" O   SER N  85 "
     model   vdw
     2.406 3.120
  ... (remaining 56031 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.040
  Set scattering table:                    0.080
  Process input model:                     20.600
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.089   7610  Z= 0.236
  Angle     :  0.746   8.487  10379  Z= 0.412
  Chirality :  0.050   0.216   1210
  Planarity :  0.005   0.051   1294
  Dihedral  : 13.417  84.023   2527
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.25), residues: 958
  helix: -0.93 (0.23), residues: 366
  sheet:  0.50 (0.34), residues: 228
  loop : -1.60 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 169 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.019   0.002   PHE R 264 
 TYR   0.012   0.001   TYR N  95 
 ARG   0.004   0.000   ARG R  64 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  247 ASP cc_start: 0.7784 (p0) cc_final: 0.7549 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.2066
  time to fit residues: 40.1549
Evaluate side-chains
  95 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0070
   chunk 45 optimal weight:    4.9990
   chunk 56 optimal weight:    7.9990
   chunk 87 optimal weight:    0.6980
   overall best weight:    0.8802

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

Flipped N/Q/H residues before XYZ refinement:
R  24 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.121649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.100253 restraints weight = 13526.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 3.69
r_work: 0.3256 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.1466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7610  Z= 0.192
  Angle     :  0.539   7.623  10379  Z= 0.288
  Chirality :  0.042   0.139   1210
  Planarity :  0.004   0.034   1294
  Dihedral  :  4.274  25.923   1059
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  :  8.95 %
    Favored  : 89.67 %
  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: -0.16 (0.26), residues: 958
  helix:  0.71 (0.27), residues: 361
  sheet:  0.83 (0.34), residues: 213
  loop : -1.44 (0.29), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 169 
 HIS   0.003   0.001   HIS R 265 
 PHE   0.013   0.001   PHE R 264 
 TYR   0.013   0.001   TYR N  95 
 ARG   0.005   0.000   ARG A 389 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: N   68 PHE cc_start: 0.7734 (m-80) cc_final: 0.7226 (m-80)
REVERT: R  250 MET cc_start: 0.7794 (mtt) cc_final: 0.7591 (mtt)
  outliers start: 10
  outliers final: 5
  residues processed: 108
  average time/residue: 0.1762
  time to fit residues: 26.8521
Evaluate side-chains
  96 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   42 ILE
Chi-restraints excluded: chain R residue  201 THR
Chi-restraints excluded: chain R residue  266 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 85 optimal weight:    0.6980
   chunk 20 optimal weight:    0.3980
   chunk 59 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0870
   chunk 65 optimal weight:    0.0670
   overall best weight:    0.3696

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

Flipped N/Q/H residues before XYZ refinement:
R  73 ASN
R  89 ASN
R 285 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.122668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.101761 restraints weight = 13707.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 3.67
r_work: 0.3289 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7610  Z= 0.132
  Angle     :  0.493   7.047  10379  Z= 0.261
  Chirality :  0.041   0.204   1210
  Planarity :  0.003   0.031   1294
  Dihedral  :  4.032  28.422   1059
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 11.02 %
    Favored  : 88.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.27), residues: 958
  helix:  1.30 (0.27), residues: 366
  sheet:  0.90 (0.34), residues: 210
  loop : -1.29 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.002   0.000   HIS A 357 
 PHE   0.011   0.001   PHE R 264 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.005   0.000   ARG A 389 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7888 (mt-10)
REVERT: B  175 GLN cc_start: 0.8248 (pp30) cc_final: 0.8038 (pp30)
REVERT: B  176 GLN cc_start: 0.8961 (mt0) cc_final: 0.8726 (tt0)
REVERT: N   68 PHE cc_start: 0.7536 (m-80) cc_final: 0.7192 (m-10)
  outliers start: 7
  outliers final: 4
  residues processed: 110
  average time/residue: 0.1782
  time to fit residues: 27.5356
Evaluate side-chains
  99 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue  201 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 95 optimal weight:    0.0000
   chunk 91 optimal weight:    0.2980
   chunk 90 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.5584

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

Flipped N/Q/H residues before XYZ refinement:
R 285 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.121503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.100878 restraints weight = 13686.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 3.64
r_work: 0.3278 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.2052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7610  Z= 0.146
  Angle     :  0.480   6.092  10379  Z= 0.256
  Chirality :  0.041   0.165   1210
  Planarity :  0.003   0.040   1294
  Dihedral  :  3.859  27.778   1059
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 11.98 %
    Favored  : 86.78 %
  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:  0.60 (0.27), residues: 958
  helix:  1.64 (0.28), residues: 367
  sheet:  0.94 (0.34), residues: 215
  loop : -1.22 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.002   0.000   HIS A 220 
 PHE   0.012   0.001   PHE R 264 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.008   0.000   ARG A 389 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7814 (mt-10)
REVERT: B  175 GLN cc_start: 0.8239 (pp30) cc_final: 0.8023 (pp30)
REVERT: G   41 CYS cc_start: 0.7115 (t) cc_final: 0.6260 (p)
REVERT: R  250 MET cc_start: 0.7988 (mtt) cc_final: 0.7643 (mtt)
  outliers start: 9
  outliers final: 5
  residues processed: 102
  average time/residue: 0.1811
  time to fit residues: 26.1582
Evaluate side-chains
  94 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue  201 THR
Chi-restraints excluded: chain R residue  266 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 61 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 4 optimal weight:    0.0370
   chunk 11 optimal weight:    0.0980
   chunk 38 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 92 optimal weight:    1.9990
   overall best weight:    1.0262

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

Flipped N/Q/H residues before XYZ refinement:
R 285 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.116562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.095952 restraints weight = 13827.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 3.59
r_work: 0.3225 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7610  Z= 0.202
  Angle     :  0.520   6.604  10379  Z= 0.279
  Chirality :  0.042   0.186   1210
  Planarity :  0.003   0.040   1294
  Dihedral  :  3.959  27.389   1059
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 13.09 %
    Favored  : 84.85 %
  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:  0.61 (0.27), residues: 958
  helix:  1.81 (0.28), residues: 361
  sheet:  1.00 (0.34), residues: 205
  loop : -1.33 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.024   0.001   PHE N  68 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.007   0.000   ARG A 389 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7822 (mt-10)
REVERT: A  210 THR cc_start: 0.6993 (OUTLIER) cc_final: 0.6757 (t)
REVERT: A  286 SER cc_start: 0.9268 (p) cc_final: 0.9045 (p)
REVERT: B  175 GLN cc_start: 0.8285 (pp30) cc_final: 0.8082 (pp30)
REVERT: B  273 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7772 (mp)
REVERT: G   21 MET cc_start: 0.5367 (tmm) cc_final: 0.5052 (tmm)
REVERT: G   41 CYS cc_start: 0.7221 (t) cc_final: 0.6407 (p)
REVERT: S    5 GLN cc_start: 0.8512 (mp10) cc_final: 0.7906 (mp10)
  outliers start: 15
  outliers final: 8
  residues processed: 109
  average time/residue: 0.1786
  time to fit residues: 27.3719
Evaluate side-chains
  104 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  309 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  201 THR
Chi-restraints excluded: chain R residue  266 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0170
   chunk 82 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 79 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
N 123 GLN
R 285 GLN
R 309 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.117497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.097241 restraints weight = 13935.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 3.59
r_work: 0.3251 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7610  Z= 0.163
  Angle     :  0.502   6.931  10379  Z= 0.267
  Chirality :  0.041   0.166   1210
  Planarity :  0.003   0.035   1294
  Dihedral  :  4.030  30.068   1059
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 15.29 %
    Favored  : 83.06 %
  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:  0.70 (0.27), residues: 958
  helix:  1.87 (0.28), residues: 367
  sheet:  0.94 (0.33), residues: 210
  loop : -1.28 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.002   0.000   HIS A 220 
 PHE   0.012   0.001   PHE N  68 
 TYR   0.009   0.001   TYR N  95 
 ARG   0.008   0.000   ARG A 389 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7796 (mt-10)
REVERT: A  211 LYS cc_start: 0.9195 (mmtp) cc_final: 0.8958 (mmtm)
REVERT: A  286 SER cc_start: 0.9264 (p) cc_final: 0.8951 (m)
REVERT: B  172 GLU cc_start: 0.8364 (mp0) cc_final: 0.8003 (mp0)
REVERT: G   41 CYS cc_start: 0.7193 (t) cc_final: 0.6395 (p)
REVERT: R  250 MET cc_start: 0.7951 (mtt) cc_final: 0.7613 (mtt)
REVERT: S    5 GLN cc_start: 0.8480 (mp10) cc_final: 0.7897 (mp10)
  outliers start: 12
  outliers final: 9
  residues processed: 106
  average time/residue: 0.1702
  time to fit residues: 25.5402
Evaluate side-chains
  105 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  201 THR
Chi-restraints excluded: chain R residue  266 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 60 optimal weight:    6.9990
   chunk 85 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 78 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 53 optimal weight:    8.9990
   chunk 44 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
R 285 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.115459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.095609 restraints weight = 14006.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 3.52
r_work: 0.3178 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7610  Z= 0.311
  Angle     :  0.592   7.923  10379  Z= 0.319
  Chirality :  0.044   0.192   1210
  Planarity :  0.004   0.038   1294
  Dihedral  :  4.294  28.911   1059
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.18 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 15.56 %
    Favored  : 82.09 %
  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 (0.27), residues: 958
  helix:  1.82 (0.27), residues: 360
  sheet:  0.82 (0.33), residues: 211
  loop : -1.42 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 211 
 HIS   0.003   0.001   HIS R  95 
 PHE   0.020   0.002   PHE R 264 
 TYR   0.013   0.001   TYR N  95 
 ARG   0.010   0.000   ARG A 389 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.863 
Fit side-chains
REVERT: A  210 THR cc_start: 0.7237 (OUTLIER) cc_final: 0.6576 (p)
REVERT: A  286 SER cc_start: 0.9336 (p) cc_final: 0.9116 (p)
REVERT: A  293 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7923 (mtpp)
REVERT: B  175 GLN cc_start: 0.8449 (pp30) cc_final: 0.8238 (pp30)
REVERT: G   41 CYS cc_start: 0.7239 (t) cc_final: 0.6500 (p)
REVERT: S    5 GLN cc_start: 0.8592 (mp10) cc_final: 0.8065 (mp10)
  outliers start: 17
  outliers final: 12
  residues processed: 108
  average time/residue: 0.1792
  time to fit residues: 27.1958
Evaluate side-chains
  107 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  201 THR
Chi-restraints excluded: chain R residue  266 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 53 optimal weight:   20.0000
   chunk 21 optimal weight:    0.2980
   chunk 77 optimal weight:    0.5980
   chunk 31 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
N 123 GLN
R  24 GLN
R 239 GLN
R 285 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.115765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.095448 restraints weight = 14070.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 3.61
r_work: 0.3198 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.2652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7610  Z= 0.220
  Angle     :  0.557   7.847  10379  Z= 0.297
  Chirality :  0.043   0.174   1210
  Planarity :  0.003   0.035   1294
  Dihedral  :  4.257  31.345   1059
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.44 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 16.53 %
    Favored  : 81.40 %
  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:  0.61 (0.27), residues: 958
  helix:  1.92 (0.28), residues: 361
  sheet:  0.82 (0.33), residues: 210
  loop : -1.36 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.015   0.001   PHE R 264 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.008   0.000   ARG A 389 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7889 (mt-10)
REVERT: A  210 THR cc_start: 0.7146 (OUTLIER) cc_final: 0.6439 (p)
REVERT: A  211 LYS cc_start: 0.9191 (mmtp) cc_final: 0.8871 (mmtm)
REVERT: A  286 SER cc_start: 0.9322 (p) cc_final: 0.9109 (p)
REVERT: A  293 LYS cc_start: 0.8123 (mmtt) cc_final: 0.7888 (mtpp)
REVERT: G   41 CYS cc_start: 0.7221 (t) cc_final: 0.6413 (p)
REVERT: S    5 GLN cc_start: 0.8618 (mp10) cc_final: 0.8007 (mp10)
  outliers start: 15
  outliers final: 9
  residues processed: 110
  average time/residue: 0.1772
  time to fit residues: 27.3652
Evaluate side-chains
  105 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  201 THR
Chi-restraints excluded: chain R residue  266 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 36 optimal weight:    0.5980
   chunk 90 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    0.2980
   chunk 21 optimal weight:    6.9990
   chunk 31 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
R 239 GLN
R 285 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.117114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.097054 restraints weight = 13968.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 3.56
r_work: 0.3269 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   7610  Z= 0.161
  Angle     :  0.526   7.646  10379  Z= 0.278
  Chirality :  0.042   0.159   1210
  Planarity :  0.003   0.035   1294
  Dihedral  :  4.080  33.067   1059
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.55 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 17.36 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.27), residues: 958
  helix:  2.12 (0.28), residues: 361
  sheet:  0.90 (0.34), residues: 210
  loop : -1.29 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.002   0.000   HIS A 357 
 PHE   0.011   0.001   PHE R 264 
 TYR   0.010   0.001   TYR N  60 
 ARG   0.009   0.000   ARG A 389 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7797 (mt-10)
REVERT: A  211 LYS cc_start: 0.9184 (mmtp) cc_final: 0.8981 (mmtm)
REVERT: A  286 SER cc_start: 0.9285 (p) cc_final: 0.9064 (p)
REVERT: A  293 LYS cc_start: 0.8065 (mmtt) cc_final: 0.7761 (mtpp)
REVERT: G   41 CYS cc_start: 0.7256 (t) cc_final: 0.6417 (p)
REVERT: S    5 GLN cc_start: 0.8557 (mp10) cc_final: 0.7948 (mp10)
  outliers start: 11
  outliers final: 10
  residues processed: 104
  average time/residue: 0.1876
  time to fit residues: 26.9942
Evaluate side-chains
  104 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  201 THR
Chi-restraints excluded: chain R residue  239 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 41 optimal weight:    7.9990
   chunk 46 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9980
   chunk 78 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 75 optimal weight:    0.7980
   chunk 88 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
N 123 GLN
R 239 GLN
R 285 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.111622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.091269 restraints weight = 14565.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 3.53
r_work: 0.3176 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7610  Z= 0.196
  Angle     :  0.535   8.124  10379  Z= 0.283
  Chirality :  0.042   0.171   1210
  Planarity :  0.003   0.040   1294
  Dihedral  :  4.088  32.690   1059
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.44 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 17.22 %
    Favored  : 81.27 %
  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:  0.77 (0.27), residues: 958
  helix:  2.11 (0.28), residues: 361
  sheet:  0.86 (0.33), residues: 210
  loop : -1.30 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.018   0.001   PHE N  68 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.009   0.000   ARG A 389 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7768 (mt-10)
REVERT: A  293 LYS cc_start: 0.8279 (mmtt) cc_final: 0.7941 (mtpp)
REVERT: B  172 GLU cc_start: 0.8403 (mp0) cc_final: 0.8117 (mp0)
REVERT: B  175 GLN cc_start: 0.8328 (pp30) cc_final: 0.8117 (pp30)
REVERT: G   41 CYS cc_start: 0.7345 (t) cc_final: 0.6507 (p)
REVERT: S    5 GLN cc_start: 0.8686 (mp10) cc_final: 0.8091 (mp10)
  outliers start: 11
  outliers final: 8
  residues processed: 103
  average time/residue: 0.1841
  time to fit residues: 26.2963
Evaluate side-chains
  103 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  201 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0060
   chunk 54 optimal weight:    0.0030
   chunk 43 optimal weight:    0.6980
   chunk 91 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0050
   chunk 77 optimal weight:    0.7980
   overall best weight:    0.2820

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

Flipped N/Q/H residues before XYZ refinement:
R 239 GLN
R 285 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.120054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.100014 restraints weight = 14105.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 3.59
r_work: 0.3306 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7610  Z= 0.137
  Angle     :  0.497   7.754  10379  Z= 0.261
  Chirality :  0.041   0.160   1210
  Planarity :  0.003   0.035   1294
  Dihedral  :  3.909  34.311   1059
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.03 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 17.77 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.28), residues: 958
  helix:  2.18 (0.28), residues: 367
  sheet:  1.06 (0.34), residues: 207
  loop : -1.23 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.016   0.001   PHE N  68 
 TYR   0.011   0.001   TYR N  60 
 ARG   0.009   0.000   ARG A 389 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3515.07 seconds
wall clock time: 63 minutes 17.62 seconds (3797.62 seconds total)