Starting phenix.real_space_refine
on Tue Mar  3 19:18:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y27_33587/03_2026/7y27_33587.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y27_33587/03_2026/7y27_33587.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y27_33587/03_2026/7y27_33587.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y27_33587/03_2026/7y27_33587.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y27_33587/03_2026/7y27_33587.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y27_33587/03_2026/7y27_33587.cif"
  }
  resolution = 3.48
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.130
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      51      5.16       5
     C    5241      2.51       5
     N    1372      2.21       5
     O    1520      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8184
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2419
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2419
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 183
          Unresolved non-hydrogen angles: 223
          Unresolved non-hydrogen dihedrals: 145
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 9, 'GLN:plan1': 6, 'ARG:plan': 11, 'ASN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 130
    Chain: "B"
      Number of atoms: 1724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1724
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 164
          Unresolved non-hydrogen angles: 193
          Unresolved non-hydrogen dihedrals: 135
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ASP:plan': 8, 'ARG:plan': 8, 'GLU:plan': 6, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 96
    Chain: "D"
      Number of atoms: 1683
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1683
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 88
          Unresolved non-hydrogen angles: 109
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 9, 'GLN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 60
    Chain: "E"
      Number of atoms: 1901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 1901
          Classifications: {'peptide': 274}
          Incomplete info: {'truncation_to_alanine': 70}
          Link IDs: {'PTRANS': 11, 'TRANS': 262}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 288
          Unresolved non-hydrogen angles: 358
          Unresolved non-hydrogen dihedrals: 257
          Unresolved non-hydrogen chiralities: 19
          Planarities with less than four sites: {'ASN:plan1': 7, 'PHE:plan': 6, 'TYR:plan': 2, 'ARG:plan': 7, 'TRP:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 147
    Chain: "F"
      Number of atoms: 327
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 327
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 91
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 44
    Chain: "C"
      Number of atoms: 102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 102
          Classifications: {'peptide': 12}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 11}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.95, per 1000 atoms: 0.24
  Number of scatterers: 8184
  At special positions: 0
  Unit cell: (93.74, 128.14, 129.86, 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      51     16.00
     O    1520      8.00
     N    1372      7.00
     C    5241      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 147 " - pdb=" SG  CYS D 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 115 " - pdb=" SG  CYS E 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   3 " - pdb=" SG  CYS C  14 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 352.1 milliseconds
  

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 14 sheets defined
      37.0% alpha, 20.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 26
      removed outlier: 3.894A  pdb=" N   LEU A   7 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 35
      removed outlier: 3.569A  pdb=" N   ILE A  33 " --> pdb=" O   THR A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 132
      removed outlier: 4.077A  pdb=" N   GLY A 131 " --> pdb=" O   THR A 128 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ASN A 132 " --> pdb=" O   ARG A 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 128 through 132'
    Processing helix  chain 'B' and resid 6 through 29
      removed outlier: 3.898A  pdb=" N   ALA B  12 " --> pdb=" O   GLU B   8 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   LYS B  29 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 32
      No H-bonds generated for 'chain 'B' and resid 30 through 32'
    Processing helix  chain 'B' and resid 45 through 55
    Processing helix  chain 'B' and resid 94 through 99
      removed outlier: 3.587A  pdb=" N   GLN B  98 " --> pdb=" O   ARG B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 131
    Processing helix  chain 'B' and resid 145 through 156
      removed outlier: 3.595A  pdb=" N   LEU B 149 " --> pdb=" O   LYS B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 164
      removed outlier: 4.124A  pdb=" N   TYR B 163 " --> pdb=" O   LYS B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 204
      removed outlier: 3.794A  pdb=" N   THR B 187 " --> pdb=" O   ASP B 183 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ILE B 200 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   SER B 201 " --> pdb=" O   PHE B 197 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   SER B 204 " --> pdb=" O   ILE B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 243
      removed outlier: 3.519A  pdb=" N   ARG B 226 " --> pdb=" O   GLU B 222 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 41 through 71
      removed outlier: 3.706A  pdb=" N   VAL E  53 " --> pdb=" O   ILE E  49 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   CYS E  54 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ILE E  55 " --> pdb=" O   PHE E  51 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ILE E  56 " --> pdb=" O   VAL E  52 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   TYR E  71 " --> pdb=" O   VAL E  67 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 77 through 95
      removed outlier: 3.901A  pdb=" N   TYR E  81 " --> pdb=" O   ILE E  77 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   GLY E  95 " --> pdb=" O   LEU E  91 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 95 through 106
      removed outlier: 4.413A  pdb=" N   LEU E  99 " --> pdb=" O   GLY E  95 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLN E 102 " --> pdb=" O   PHE E  98 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   VAL E 103 " --> pdb=" O   LEU E  99 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 111 through 146
      removed outlier: 4.306A  pdb=" N   CYS E 115 " --> pdb=" O   GLY E 111 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   ARG E 116 " --> pdb=" O   LYS E 112 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   VAL E 117 " --> pdb=" O   ALA E 113 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ILE E 130 " --> pdb=" O   GLN E 126 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   PHE E 131 " --> pdb=" O   PHE E 127 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 149 through 154
      removed outlier: 3.850A  pdb=" N   TRP E 153 " --> pdb=" O   LYS E 149 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 155 through 174
      removed outlier: 3.842A  pdb=" N   ALA E 159 " --> pdb=" O   ARG E 155 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   LYS E 160 " --> pdb=" O   PRO E 156 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   THR E 163 " --> pdb=" O   ALA E 159 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   MET E 164 " --> pdb=" O   LYS E 160 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 174 through 180
      removed outlier: 3.502A  pdb=" N   TYR E 180 " --> pdb=" O   PRO E 176 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 203 through 215
      removed outlier: 3.610A  pdb=" N   LEU E 215 " --> pdb=" O   TYR E 211 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 217 through 238
      removed outlier: 3.643A  pdb=" N   THR E 222 " --> pdb=" O   LEU E 218 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 250 through 282
      removed outlier: 3.740A  pdb=" N   VAL E 254 " --> pdb=" O   SER E 250 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ARG E 256 " --> pdb=" O   LYS E 252 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   ALA E 263 " --> pdb=" O   SER E 259 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   PHE E 265 " --> pdb=" O   VAL E 261 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   TRP E 269 " --> pdb=" O   PHE E 265 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU E 270 " --> pdb=" O   ILE E 266 " (cutoff:3.500A)
      Proline residue:  E 271  - end of helix
      removed outlier: 3.694A  pdb=" N   VAL E 277 " --> pdb=" O   TYR E 273 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 287 through 313
      removed outlier: 3.561A  pdb=" N   PHE E 296 " --> pdb=" O   GLY E 292 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   VAL E 297 " --> pdb=" O   MET E 293 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   VAL E 298 " --> pdb=" O   PHE E 294 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL E 299 " --> pdb=" O   ASP E 295 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   ASN E 304 " --> pdb=" O   LEU E 300 " (cutoff:3.500A)
      removed outlier: 5.024A  pdb=" N   SER E 305 " --> pdb=" O   THR E 301 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   CYS E 306 " --> pdb=" O   TYR E 302 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ALA E 307 " --> pdb=" O   ALA E 303 " (cutoff:3.500A)
      Proline residue:  E 309  - end of helix
      removed outlier: 3.631A  pdb=" N   TYR E 312 " --> pdb=" O   ASN E 308 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 316 through 324
      removed outlier: 3.796A  pdb=" N   GLN E 324 " --> pdb=" O   LYS E 320 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 12 through 24
      removed outlier: 3.591A  pdb=" N   ASN F  24 " --> pdb=" O   LYS F  20 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 29 through 44
      removed outlier: 3.559A  pdb=" N   ALA F  33 " --> pdb=" O   LYS F  29 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   HIS F  44 " --> pdb=" O   TYR F  40 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 50
      removed outlier: 3.765A  pdb=" N   ARG A  46 " --> pdb=" O   ASN A 340 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ASN A 340 " --> pdb=" O   ARG A  46 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ARG A  48 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   ILE A 338 " --> pdb=" O   ARG A  48 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   CYS A 317 " --> pdb=" O   GLY A 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 63
      removed outlier: 3.563A  pdb=" N   TYR A  59 " --> pdb=" O   ALA A  73 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   ALA A  73 " --> pdb=" O   TYR A  59 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   MET A  61 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   VAL A  71 " --> pdb=" O   MET A  61 " (cutoff:3.500A)
      removed outlier: 5.140A  pdb=" N   TRP A  63 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   LEU A  69 " --> pdb=" O   TRP A  63 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   SER A  74 " --> pdb=" O   LYS A  78 " (cutoff:3.500A)
      removed outlier: 5.019A  pdb=" N   LYS A  78 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   HIS A  91 " --> pdb=" O   ILE A  81 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ASP A  83 " --> pdb=" O   LYS A  89 " (cutoff:3.500A)
      removed outlier: 5.876A  pdb=" N   LYS A  89 " --> pdb=" O   ASP A  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 105
      removed outlier: 3.691A  pdb=" N   THR A 102 " --> pdb=" O   GLY A 115 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   GLY A 115 " --> pdb=" O   THR A 102 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   CYS A 121 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   GLU A 138 " --> pdb=" O   CYS A 121 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ILE A 123 " --> pdb=" O   SER A 136 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ASN A 125 " --> pdb=" O   ARG A 134 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   ARG A 134 " --> pdb=" O   ASN A 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 151
      removed outlier: 3.947A  pdb=" N   ILE A 157 " --> pdb=" O   TRP A 169 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   THR A 165 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   CYS A 166 " --> pdb=" O   PHE A 180 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   THR A 178 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 190
      removed outlier: 6.496A  pdb=" N   GLY A 202 " --> pdb=" O   MET A 188 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   LEU A 190 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   VAL A 200 " --> pdb=" O   LEU A 190 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LYS A 209 " --> pdb=" O   SER A 201 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA A 203 " --> pdb=" O   SER A 207 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   SER A 207 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLN A 220 " --> pdb=" O   LEU A 210 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 229 through 234
      removed outlier: 7.063A  pdb=" N   GLY A 244 " --> pdb=" O   ASN A 230 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   ILE A 232 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   ALA A 242 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   PHE A 253 " --> pdb=" O   PHE A 241 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LEU A 252 " --> pdb=" O   MET A 262 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   MET A 262 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   ASP A 254 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   GLU A 260 " --> pdb=" O   ASP A 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 276 through 278
      removed outlier: 3.558A  pdb=" N   LEU A 308 " --> pdb=" O   CYS A 294 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLY A 306 " --> pdb=" O   VAL A 296 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   ASP A 298 " --> pdb=" O   ARG A 304 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ARG A 304 " --> pdb=" O   ASP A 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 69 through 76
      removed outlier: 4.878A  pdb=" N   VAL B  86 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   GLY B  40 " --> pdb=" O   VAL B  86 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   ALA B 105 " --> pdb=" O   ARG B  35 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU B  37 " --> pdb=" O   ALA B 105 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL B 110 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ASN B 144 " --> pdb=" O   VAL B 110 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   TYR B 212 " --> pdb=" O   VAL B 139 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'D' and resid 58 through 60
      removed outlier: 5.346A  pdb=" N   TRP D  47 " --> pdb=" O   ARG D  38 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   ARG D  38 " --> pdb=" O   TRP D  47 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA D  49 " --> pdb=" O   TRP D  36 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER D  99 " --> pdb=" O   GLY D  33 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   HIS D  35 " --> pdb=" O   VAL D  97 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   VAL D  97 " --> pdb=" O   HIS D  35 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 128 through 130
    Processing sheet with id=AB3, first strand: chain 'D' and resid 134 through 136
      removed outlier: 6.710A  pdb=" N   VAL D 135 " --> pdb=" O   GLU D 234 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ILE D 177 " --> pdb=" O   TRP D 164 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   LEU D 166 " --> pdb=" O   LEU D 175 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   LEU D 175 " --> pdb=" O   LEU D 166 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 184 through 186
    Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 7
      removed outlier: 4.571A  pdb=" N   ASN C   5 " --> pdb=" O   THR C  12 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   THR C  12 " --> pdb=" O   ASN C   5 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   PHE C   7 " --> pdb=" O   THR C  10 " (cutoff:3.500A)

    386 hydrogen bonds defined for protein.
    1092 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.33

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.05 -     1.20: 3
        1.20 -     1.36: 2665
        1.36 -     1.51: 2456
        1.51 -     1.66: 3163
        1.66 -     1.82: 74
  Bond restraints: 8361
  Sorted by residual:
  bond pdb=" C10 CLR E 401 "
       pdb=" C9  CLR E 401 "
    ideal  model  delta    sigma   weight residual
    1.551  1.052  0.499 2.00e-02 2.50e+03 6.24e+02
  bond pdb=" C1  CLR E 401 "
       pdb=" C10 CLR E 401 "
    ideal  model  delta    sigma   weight residual
    1.544  1.125  0.419 2.00e-02 2.50e+03 4.39e+02
  bond pdb=" C6  CLR E 401 "
       pdb=" C7  CLR E 401 "
    ideal  model  delta    sigma   weight residual
    1.492  1.089  0.403 2.00e-02 2.50e+03 4.05e+02
  bond pdb=" C3  CLR E 401 "
       pdb=" C4  CLR E 401 "
    ideal  model  delta    sigma   weight residual
    1.526  1.209  0.317 2.00e-02 2.50e+03 2.50e+02
  bond pdb=" C13 CLR E 401 "
       pdb=" C17 CLR E 401 "
    ideal  model  delta    sigma   weight residual
    1.550  1.253  0.297 2.00e-02 2.50e+03 2.21e+02
  ... (remaining 8356 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 11320
        2.45 -     4.89: 99
        4.89 -     7.34: 16
        7.34 -     9.79: 3
        9.79 -    12.23: 2
  Bond angle restraints: 11440
  Sorted by residual:
  angle pdb=" N   ILE A 270 "
        pdb=" CA  ILE A 270 "
        pdb=" C   ILE A 270 "
      ideal   model   delta    sigma   weight residual
     113.71  108.69    5.02 9.50e-01 1.11e+00 2.79e+01
  angle pdb=" C4  CLR E 401 "
        pdb=" C5  CLR E 401 "
        pdb=" C6  CLR E 401 "
      ideal   model   delta    sigma   weight residual
     120.33  108.10   12.23 3.00e+00 1.11e-01 1.66e+01
  angle pdb=" C   LEU E 105 "
        pdb=" N   VAL E 106 "
        pdb=" CA  VAL E 106 "
      ideal   model   delta    sigma   weight residual
     121.97  129.29   -7.32 1.80e+00 3.09e-01 1.66e+01
  angle pdb=" CA  GLU A 130 "
        pdb=" CB  GLU A 130 "
        pdb=" CG  GLU A 130 "
      ideal   model   delta    sigma   weight residual
     114.10  121.89   -7.79 2.00e+00 2.50e-01 1.52e+01
  angle pdb=" CA  PRO B 165 "
        pdb=" N   PRO B 165 "
        pdb=" CD  PRO B 165 "
      ideal   model   delta    sigma   weight residual
     112.00  106.75    5.25 1.40e+00 5.10e-01 1.40e+01
  ... (remaining 11435 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.35: 4560
       19.35 -    38.70: 276
       38.70 -    58.06: 45
       58.06 -    77.41: 9
       77.41 -    96.76: 6
  Dihedral angle restraints: 4896
    sinusoidal: 1603
      harmonic: 3293
  Sorted by residual:
  dihedral pdb=" CB  CYS C   3 "
           pdb=" SG  CYS C   3 "
           pdb=" SG  CYS C  14 "
           pdb=" CB  CYS C  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    2.41  -88.41     1      1.00e+01 1.00e-02 9.33e+01
  dihedral pdb=" CB  CYS D 147 "
           pdb=" SG  CYS D 147 "
           pdb=" SG  CYS D 217 "
           pdb=" CB  CYS D 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.90  -37.90     1      1.00e+01 1.00e-02 2.02e+01
  dihedral pdb=" CA  PHE E 217 "
           pdb=" C   PHE E 217 "
           pdb=" N   LEU E 218 "
           pdb=" CA  LEU E 218 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.36  -19.64     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 4893 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.334: 1364
       0.334 -    0.668: 2
       0.668 -    1.001: 0
       1.001 -    1.335: 0
       1.335 -    1.669: 1
  Chirality restraints: 1367
  Sorted by residual:
  chirality pdb=" C10 CLR E 401 "
            pdb=" C1  CLR E 401 "
            pdb=" C5  CLR E 401 "
            pdb=" C9  CLR E 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -1.18   -1.67 2.00e-01 2.50e+01 6.96e+01
  chirality pdb=" C9  CLR E 401 "
            pdb=" C10 CLR E 401 "
            pdb=" C11 CLR E 401 "
            pdb=" C8  CLR E 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.10   -0.35 2.00e-01 2.50e+01 3.05e+00
  chirality pdb=" C3  CLR E 401 "
            pdb=" C2  CLR E 401 "
            pdb=" C4  CLR E 401 "
            pdb=" O1  CLR E 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.46   -2.12   -0.34 2.00e-01 2.50e+01 2.85e+00
  ... (remaining 1364 not shown)

  Planarity restraints: 1450
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU E 175 "   -0.038 5.00e-02 4.00e+02   5.73e-02 5.25e+00
        pdb=" N   PRO E 176 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO E 176 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO E 176 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 244 "    0.010 2.00e-02 2.50e+03   2.04e-02 4.17e+00
        pdb=" C   ASN B 244 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   ASN B 244 "    0.013 2.00e-02 2.50e+03
        pdb=" N   LEU B 245 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL E 219 "    0.026 5.00e-02 4.00e+02   3.91e-02 2.44e+00
        pdb=" N   PRO E 220 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO E 220 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO E 220 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1447 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 676
        2.74 -     3.28: 7875
        3.28 -     3.82: 12249
        3.82 -     4.36: 12717
        4.36 -     4.90: 24077
  Nonbonded interactions: 57594
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 163 "
            pdb=" OG1 THR A 165 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" O   ASN B 244 "
            pdb=" ND2 ASN B 244 "
     model   vdw
     2.229 3.120
  nonbonded pdb=" ND2 ASN A 230 "
            pdb=" OD1 ASP A 246 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" O   PHE E 275 "
            pdb=" OG  SER E 278 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OD1 ASP A 247 "
            pdb=" OG1 THR A 249 "
     model   vdw
     2.266 3.040
  ... (remaining 57589 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:             1.030
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.570
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
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      :  0.012   0.499   8364  Z= 0.616
  Angle     :  0.626  12.233  11446  Z= 0.332
  Chirality :  0.062   1.669   1367
  Planarity :  0.004   0.057   1450
  Dihedral  : 13.374  96.759   2759
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.68 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.25), residues: 1115
  helix:  2.02 (0.28), residues: 358
  sheet:  0.09 (0.31), residues: 284
  loop : -1.42 (0.27), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 168 
 TYR   0.013   0.001   TYR E 180 
 PHE   0.011   0.001   PHE B  70 
 TRP   0.010   0.001   TRP E 269 
 HIS   0.003   0.001   HIS F  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.01237 ( 8361)
  covalent geometry    : angle       0.62523 (11440)
  SS BOND              : bond        0.00531 (    3)
  SS BOND              : angle       1.06645 (    6)
  hydrogen bonds       : bond        0.16388 (  386)
  hydrogen bonds       : angle       5.88848 ( 1092)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A  259 GLN cc_start: 0.8124 (pt0) cc_final: 0.7886 (pt0)
REVERT: B  167 PHE cc_start: 0.7579 (t80) cc_final: 0.7187 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.0863
  time to fit residues: 19.3002
Evaluate side-chains
  127 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.2980
   chunk 106 optimal weight:   10.0000
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 146 GLN
B 244 ASN
D 171 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.154262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.117298 restraints weight = 14305.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 3.91
r_work: 0.3356 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.1198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8364  Z= 0.136
  Angle     :  0.564   7.319  11446  Z= 0.301
  Chirality :  0.041   0.148   1367
  Planarity :  0.004   0.052   1450
  Dihedral  :  4.596  41.483   1267
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.59 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  8.80 %
    Favored  : 90.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.26), residues: 1115
  helix:  2.58 (0.27), residues: 359
  sheet:  0.16 (0.31), residues: 294
  loop : -1.51 (0.27), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 251 
 TYR   0.015   0.001   TYR D 178 
 PHE   0.010   0.001   PHE A 199 
 TRP   0.012   0.001   TRP B 129 
 HIS   0.003   0.001   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8361)
  covalent geometry    : angle       0.56401 (11440)
  SS BOND              : bond        0.00704 (    3)
  SS BOND              : angle       0.93602 (    6)
  hydrogen bonds       : bond        0.04862 (  386)
  hydrogen bonds       : angle       4.42669 ( 1092)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 142
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A  259 GLN cc_start: 0.8048 (pt0) cc_final: 0.7848 (pt0)
REVERT: B   43 ASN cc_start: 0.7532 (t0) cc_final: 0.7261 (t0)
REVERT: B  167 PHE cc_start: 0.7629 (t80) cc_final: 0.7293 (t80)
REVERT: B  188 ARG cc_start: 0.7321 (tpt-90) cc_final: 0.6535 (tpt-90)
REVERT: D  159 ASN cc_start: 0.9074 (m110) cc_final: 0.8809 (m110)
  outliers start: 6
  outliers final: 5
  residues processed: 145
  average time/residue: 0.0740
  time to fit residues: 15.7058
Evaluate side-chains
  144 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 139
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  201 THR
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue  278 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0670
   chunk 80 optimal weight:    7.9990
   chunk 7 optimal weight:    0.8980
   chunk 0 optimal weight:   70.0000
   chunk 74 optimal weight:    0.0000
   chunk 105 optimal weight:    5.9990
   chunk 16 optimal weight:    8.9990
   chunk 29 optimal weight:    8.9990
   chunk 71 optimal weight:    6.9990
   chunk 69 optimal weight:   20.0000
   overall best weight:    1.5926

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
B  75 GLN
D 171 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.152980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.115934 restraints weight = 14073.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 3.89
r_work: 0.3349 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8364  Z= 0.130
  Angle     :  0.535   7.047  11446  Z= 0.287
  Chirality :  0.040   0.136   1367
  Planarity :  0.004   0.046   1450
  Dihedral  :  4.259  31.745   1267
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.68 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 11.77 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.26), residues: 1115
  helix:  2.73 (0.27), residues: 360
  sheet:  0.10 (0.31), residues: 296
  loop : -1.45 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 168 
 TYR   0.014   0.001   TYR D 178 
 PHE   0.010   0.001   PHE A 199 
 TRP   0.011   0.001   TRP B 129 
 HIS   0.004   0.001   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8361)
  covalent geometry    : angle       0.53459 (11440)
  SS BOND              : bond        0.00765 (    3)
  SS BOND              : angle       0.73684 (    6)
  hydrogen bonds       : bond        0.04735 (  386)
  hydrogen bonds       : angle       4.22307 ( 1092)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A  259 GLN cc_start: 0.8052 (pt0) cc_final: 0.7808 (pt0)
REVERT: B   43 ASN cc_start: 0.7584 (t0) cc_final: 0.7334 (t0)
REVERT: B  111 ASP cc_start: 0.8776 (t0) cc_final: 0.8532 (t0)
REVERT: B  167 PHE cc_start: 0.7646 (t80) cc_final: 0.7273 (t80)
REVERT: B  188 ARG cc_start: 0.7285 (tpt-90) cc_final: 0.6396 (tpt-90)
REVERT: D  159 ASN cc_start: 0.9031 (m110) cc_final: 0.8651 (m110)
  outliers start: 15
  outliers final: 10
  residues processed: 148
  average time/residue: 0.0759
  time to fit residues: 16.3129
Evaluate side-chains
  145 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 135
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  201 THR
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  281 SER
Chi-restraints excluded: chain E residue  299 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 72 optimal weight:    8.9990
   chunk 65 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
E  79 ASN
E  84 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.148174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.106728 restraints weight = 14469.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 3.93
r_work: 0.3304 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8364  Z= 0.158
  Angle     :  0.569   6.915  11446  Z= 0.306
  Chirality :  0.042   0.137   1367
  Planarity :  0.004   0.044   1450
  Dihedral  :  4.381  29.784   1267
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.13 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 13.84 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.26), residues: 1115
  helix:  2.64 (0.27), residues: 361
  sheet: -0.01 (0.31), residues: 304
  loop : -1.43 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  18 
 TYR   0.014   0.001   TYR D 178 
 PHE   0.011   0.001   PHE D 165 
 TRP   0.009   0.001   TRP B 129 
 HIS   0.005   0.002   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 8361)
  covalent geometry    : angle       0.56926 (11440)
  SS BOND              : bond        0.00838 (    3)
  SS BOND              : angle       0.84310 (    6)
  hydrogen bonds       : bond        0.05291 (  386)
  hydrogen bonds       : angle       4.32165 ( 1092)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A  151 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8400 (m-80)
REVERT: A  228 ASP cc_start: 0.8240 (m-30) cc_final: 0.7556 (m-30)
REVERT: A  254 ASP cc_start: 0.8785 (t0) cc_final: 0.8070 (m-30)
REVERT: B   43 ASN cc_start: 0.7660 (t0) cc_final: 0.7372 (t0)
REVERT: B  167 PHE cc_start: 0.7631 (t80) cc_final: 0.7250 (t80)
REVERT: B  188 ARG cc_start: 0.7307 (tpt-90) cc_final: 0.6368 (tpt-90)
REVERT: B  233 ASP cc_start: 0.8909 (t0) cc_final: 0.8676 (t0)
REVERT: D   34 MET cc_start: 0.8631 (mmm) cc_final: 0.8404 (mmm)
REVERT: D  159 ASN cc_start: 0.9051 (m110) cc_final: 0.8679 (m110)
REVERT: D  221 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8390 (tt)
  outliers start: 21
  outliers final: 14
  residues processed: 151
  average time/residue: 0.0773
  time to fit residues: 16.8789
Evaluate side-chains
  148 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  146 GLN
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   19 LYS
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  201 THR
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue  193 CYS
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  299 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9980
   chunk 52 optimal weight:    8.9990
   chunk 66 optimal weight:    4.9990
   chunk 0 optimal weight:   70.0000
   chunk 5 optimal weight:    3.9990
   chunk 106 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 79 optimal weight:   20.0000
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.151817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.114258 restraints weight = 14300.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 3.98
r_work: 0.3320 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8364  Z= 0.128
  Angle     :  0.539   6.470  11446  Z= 0.286
  Chirality :  0.040   0.135   1367
  Planarity :  0.004   0.043   1450
  Dihedral  :  4.257  29.734   1267
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.04 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 14.75 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.26), residues: 1115
  helix:  2.75 (0.27), residues: 361
  sheet:  0.03 (0.31), residues: 297
  loop : -1.41 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  18 
 TYR   0.013   0.001   TYR D 178 
 PHE   0.010   0.001   PHE A 199 
 TRP   0.007   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8361)
  covalent geometry    : angle       0.53868 (11440)
  SS BOND              : bond        0.00740 (    3)
  SS BOND              : angle       0.75277 (    6)
  hydrogen bonds       : bond        0.04635 (  386)
  hydrogen bonds       : angle       4.16046 ( 1092)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 0.304 
Fit side-chains
REVERT: A  151 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8338 (m-80)
REVERT: A  228 ASP cc_start: 0.8224 (m-30) cc_final: 0.7566 (m-30)
REVERT: A  254 ASP cc_start: 0.8731 (t0) cc_final: 0.8031 (m-30)
REVERT: B   43 ASN cc_start: 0.7618 (t0) cc_final: 0.7319 (t0)
REVERT: B  167 PHE cc_start: 0.7629 (t80) cc_final: 0.7107 (t80)
REVERT: D   34 MET cc_start: 0.8653 (mmm) cc_final: 0.8432 (mmm)
REVERT: D  159 ASN cc_start: 0.9021 (m110) cc_final: 0.8638 (m110)
  outliers start: 17
  outliers final: 13
  residues processed: 141
  average time/residue: 0.0749
  time to fit residues: 15.4414
Evaluate side-chains
  148 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 134
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain B residue   53 MET
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  201 THR
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  299 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 77 optimal weight:    0.4980
   chunk 35 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 29 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 69 optimal weight:   20.0000
   chunk 24 optimal weight:    3.9990
   chunk 111 optimal weight:    0.0570
   chunk 26 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   overall best weight:    0.8700

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.155089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.115770 restraints weight = 14004.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 3.73
r_work: 0.3379 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8364  Z= 0.099
  Angle     :  0.507   6.097  11446  Z= 0.265
  Chirality :  0.039   0.136   1367
  Planarity :  0.003   0.042   1450
  Dihedral  :  4.012  29.502   1267
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.32 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.14 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.26), residues: 1115
  helix:  2.94 (0.27), residues: 361
  sheet:  0.19 (0.31), residues: 294
  loop : -1.37 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  18 
 TYR   0.013   0.001   TYR D 178 
 PHE   0.010   0.001   PHE C   6 
 TRP   0.007   0.001   TRP B 129 
 HIS   0.003   0.001   HIS E 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 8361)
  covalent geometry    : angle       0.50666 (11440)
  SS BOND              : bond        0.00560 (    3)
  SS BOND              : angle       0.65560 (    6)
  hydrogen bonds       : bond        0.03685 (  386)
  hydrogen bonds       : angle       3.92556 ( 1092)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
REVERT: A  151 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8241 (m-80)
REVERT: A  228 ASP cc_start: 0.8095 (m-30) cc_final: 0.7454 (m-30)
REVERT: A  254 ASP cc_start: 0.8648 (t0) cc_final: 0.7931 (m-30)
REVERT: B   43 ASN cc_start: 0.7631 (t0) cc_final: 0.7347 (t0)
REVERT: B   85 ASP cc_start: 0.7828 (p0) cc_final: 0.7539 (p0)
REVERT: B  111 ASP cc_start: 0.8739 (t0) cc_final: 0.8507 (t0)
REVERT: B  167 PHE cc_start: 0.7621 (t80) cc_final: 0.7104 (t80)
REVERT: B  233 ASP cc_start: 0.8906 (t0) cc_final: 0.8454 (t0)
REVERT: D  221 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8266 (tt)
  outliers start: 16
  outliers final: 11
  residues processed: 152
  average time/residue: 0.0787
  time to fit residues: 17.0795
Evaluate side-chains
  148 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 135
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain B residue   53 MET
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  299 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 75 optimal weight:   10.0000
   chunk 52 optimal weight:    9.9990
   chunk 91 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 47 optimal weight:   10.0000
   chunk 85 optimal weight:    2.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 159 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.149427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.112193 restraints weight = 14496.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 4.03
r_work: 0.3289 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8364  Z= 0.182
  Angle     :  0.587   6.253  11446  Z= 0.316
  Chirality :  0.042   0.219   1367
  Planarity :  0.004   0.042   1450
  Dihedral  :  4.363  29.615   1267
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.75 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.04 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.26), residues: 1115
  helix:  2.69 (0.27), residues: 362
  sheet: -0.04 (0.30), residues: 305
  loop : -1.43 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  18 
 TYR   0.014   0.001   TYR E  50 
 PHE   0.013   0.001   PHE D 165 
 TRP   0.009   0.001   TRP A  82 
 HIS   0.005   0.002   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 8361)
  covalent geometry    : angle       0.58689 (11440)
  SS BOND              : bond        0.00866 (    3)
  SS BOND              : angle       0.84721 (    6)
  hydrogen bonds       : bond        0.05460 (  386)
  hydrogen bonds       : angle       4.30166 ( 1092)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
REVERT: A  151 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.8441 (m-80)
REVERT: A  215 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6883 (tt0)
REVERT: A  228 ASP cc_start: 0.8295 (m-30) cc_final: 0.7528 (m-30)
REVERT: A  254 ASP cc_start: 0.8761 (t0) cc_final: 0.7943 (m-30)
REVERT: B   43 ASN cc_start: 0.7761 (t0) cc_final: 0.7428 (t0)
REVERT: B   85 ASP cc_start: 0.7966 (p0) cc_final: 0.7673 (p0)
REVERT: B   94 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8182 (tpt-90)
REVERT: B  123 ASN cc_start: 0.7859 (m110) cc_final: 0.7645 (m-40)
REVERT: B  167 PHE cc_start: 0.7599 (t80) cc_final: 0.7257 (t80)
REVERT: B  188 ARG cc_start: 0.7288 (tpt-90) cc_final: 0.6397 (tpt-90)
REVERT: B  233 ASP cc_start: 0.8974 (t0) cc_final: 0.8684 (t0)
REVERT: D  221 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8406 (tt)
  outliers start: 20
  outliers final: 16
  residues processed: 148
  average time/residue: 0.0783
  time to fit residues: 16.6373
Evaluate side-chains
  152 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain B residue   53 MET
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue   94 ARG
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  146 GLN
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   19 LYS
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue  193 CYS
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  280 VAL
Chi-restraints excluded: chain E residue  299 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 80 optimal weight:    7.9990
   chunk 52 optimal weight:    9.9990
   chunk 46 optimal weight:    0.9980
   chunk 29 optimal weight:    7.9990
   chunk 70 optimal weight:    4.9990
   chunk 106 optimal weight:    4.9990
   chunk 9 optimal weight:    8.9990
   chunk 78 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 71 optimal weight:    0.7980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 142 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.150424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.109036 restraints weight = 14294.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 3.93
r_work: 0.3336 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.2096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8364  Z= 0.113
  Angle     :  0.533   6.628  11446  Z= 0.281
  Chirality :  0.040   0.166   1367
  Planarity :  0.004   0.041   1450
  Dihedral  :  4.128  29.616   1267
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.68 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 16.82 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.26), residues: 1115
  helix:  2.77 (0.27), residues: 366
  sheet:  0.05 (0.31), residues: 291
  loop : -1.43 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  18 
 TYR   0.012   0.001   TYR D 178 
 PHE   0.010   0.001   PHE A 199 
 TRP   0.006   0.001   TRP E 269 
 HIS   0.003   0.001   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 8361)
  covalent geometry    : angle       0.53332 (11440)
  SS BOND              : bond        0.00642 (    3)
  SS BOND              : angle       0.69164 (    6)
  hydrogen bonds       : bond        0.04084 (  386)
  hydrogen bonds       : angle       4.00387 ( 1092)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A  151 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8320 (m-80)
REVERT: A  228 ASP cc_start: 0.8248 (m-30) cc_final: 0.7467 (m-30)
REVERT: A  254 ASP cc_start: 0.8691 (t0) cc_final: 0.7903 (m-30)
REVERT: B   43 ASN cc_start: 0.7692 (t0) cc_final: 0.7364 (t0)
REVERT: B   94 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8092 (tpt-90)
REVERT: B  111 ASP cc_start: 0.8742 (t0) cc_final: 0.8486 (t0)
REVERT: B  123 ASN cc_start: 0.7811 (m110) cc_final: 0.7594 (m-40)
REVERT: B  167 PHE cc_start: 0.7605 (t80) cc_final: 0.7222 (t80)
REVERT: B  188 ARG cc_start: 0.7213 (tpt-90) cc_final: 0.6318 (tpt-90)
REVERT: D  159 ASN cc_start: 0.9059 (m-40) cc_final: 0.8684 (m110)
REVERT: D  221 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8303 (tt)
  outliers start: 18
  outliers final: 13
  residues processed: 143
  average time/residue: 0.0837
  time to fit residues: 17.0057
Evaluate side-chains
  145 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain B residue   53 MET
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain B residue   94 ARG
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  146 GLN
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  280 VAL
Chi-restraints excluded: chain E residue  299 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0170
   chunk 58 optimal weight:    9.9990
   chunk 69 optimal weight:   40.0000
   chunk 14 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 64 optimal weight:    9.9990
   overall best weight:    2.2026

-------------------------------------------------------------------------------
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 = 0.3925 r_free = 0.3925 target = 0.150303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.113393 restraints weight = 14498.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 3.88
r_work: 0.3306 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8364  Z= 0.159
  Angle     :  0.571   6.534  11446  Z= 0.305
  Chirality :  0.041   0.137   1367
  Planarity :  0.004   0.040   1450
  Dihedral  :  4.309  29.830   1267
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 16.56 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.26), residues: 1115
  helix:  2.66 (0.27), residues: 365
  sheet: -0.10 (0.31), residues: 297
  loop : -1.48 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  18 
 TYR   0.013   0.001   TYR E  50 
 PHE   0.010   0.001   PHE A 222 
 TRP   0.007   0.001   TRP A  82 
 HIS   0.005   0.001   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 8361)
  covalent geometry    : angle       0.57090 (11440)
  SS BOND              : bond        0.00811 (    3)
  SS BOND              : angle       0.75677 (    6)
  hydrogen bonds       : bond        0.05091 (  386)
  hydrogen bonds       : angle       4.20555 ( 1092)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  151 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8418 (m-80)
REVERT: A  215 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6895 (tt0)
REVERT: A  228 ASP cc_start: 0.8277 (m-30) cc_final: 0.7502 (m-30)
REVERT: A  254 ASP cc_start: 0.8709 (t0) cc_final: 0.7875 (m-30)
REVERT: B   43 ASN cc_start: 0.7727 (t0) cc_final: 0.7387 (t0)
REVERT: B   94 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8138 (tpt-90)
REVERT: B  123 ASN cc_start: 0.7862 (m110) cc_final: 0.7644 (m-40)
REVERT: B  167 PHE cc_start: 0.7601 (t80) cc_final: 0.7268 (t80)
REVERT: B  188 ARG cc_start: 0.7245 (tpt-90) cc_final: 0.6502 (tpt170)
REVERT: D  159 ASN cc_start: 0.9060 (m-40) cc_final: 0.8673 (m110)
REVERT: D  221 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8366 (tt)
  outliers start: 22
  outliers final: 17
  residues processed: 138
  average time/residue: 0.0828
  time to fit residues: 16.0297
Evaluate side-chains
  149 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain B residue   53 MET
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain B residue   94 ARG
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  146 GLN
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   19 LYS
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  201 THR
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue  195 ILE
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  280 VAL
Chi-restraints excluded: chain E residue  299 VAL
Chi-restraints excluded: chain F residue   28 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 68 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 2 optimal weight:   20.0000
   chunk 22 optimal weight:    9.9990
   chunk 32 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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 = 0.3919 r_free = 0.3919 target = 0.149185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.112476 restraints weight = 14297.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 3.84
r_work: 0.3296 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8364  Z= 0.169
  Angle     :  0.586   6.444  11446  Z= 0.314
  Chirality :  0.042   0.135   1367
  Planarity :  0.004   0.041   1450
  Dihedral  :  4.435  29.654   1267
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 16.69 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.26), residues: 1115
  helix:  2.55 (0.27), residues: 366
  sheet: -0.15 (0.31), residues: 296
  loop : -1.49 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  18 
 TYR   0.014   0.001   TYR E  50 
 PHE   0.010   0.001   PHE A 222 
 TRP   0.008   0.001   TRP A  82 
 HIS   0.005   0.001   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 8361)
  covalent geometry    : angle       0.58572 (11440)
  SS BOND              : bond        0.00875 (    3)
  SS BOND              : angle       0.81513 (    6)
  hydrogen bonds       : bond        0.05282 (  386)
  hydrogen bonds       : angle       4.27393 ( 1092)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 0.319 
Fit side-chains
REVERT: A  151 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8419 (m-80)
REVERT: A  215 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6867 (tt0)
REVERT: A  228 ASP cc_start: 0.8323 (m-30) cc_final: 0.7558 (m-30)
REVERT: A  254 ASP cc_start: 0.8754 (t0) cc_final: 0.7922 (m-30)
REVERT: B   43 ASN cc_start: 0.7725 (t0) cc_final: 0.7390 (t0)
REVERT: B   85 ASP cc_start: 0.7929 (p0) cc_final: 0.7642 (p0)
REVERT: B   94 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8225 (tpt-90)
REVERT: B  123 ASN cc_start: 0.7895 (m110) cc_final: 0.7676 (m-40)
REVERT: B  167 PHE cc_start: 0.7567 (t80) cc_final: 0.7205 (t80)
REVERT: B  188 ARG cc_start: 0.7272 (tpt-90) cc_final: 0.6526 (tpt170)
REVERT: B  233 ASP cc_start: 0.8978 (t0) cc_final: 0.8696 (t0)
REVERT: D  159 ASN cc_start: 0.9040 (m-40) cc_final: 0.8622 (m110)
REVERT: D  221 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8380 (tt)
  outliers start: 23
  outliers final: 18
  residues processed: 149
  average time/residue: 0.0803
  time to fit residues: 16.8802
Evaluate side-chains
  149 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain B residue   53 MET
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain B residue   94 ARG
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   19 LYS
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  201 THR
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue  107 HIS
Chi-restraints excluded: chain E residue  193 CYS
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  280 VAL
Chi-restraints excluded: chain E residue  299 VAL
Chi-restraints excluded: chain F residue   28 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 64 optimal weight:    9.9990
   chunk 66 optimal weight:    0.5980
   chunk 44 optimal weight:    7.9990
   chunk 18 optimal weight:    6.9990
   chunk 86 optimal weight:    6.9990
   chunk 84 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   chunk 22 optimal weight:   10.0000
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
B 244 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.152643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.112662 restraints weight = 14376.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 3.82
r_work: 0.3335 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.2290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8364  Z= 0.119
  Angle     :  0.544   7.155  11446  Z= 0.287
  Chirality :  0.040   0.135   1367
  Planarity :  0.004   0.040   1450
  Dihedral  :  4.159  29.783   1267
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.59 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.26), residues: 1115
  helix:  2.79 (0.27), residues: 365
  sheet: -0.02 (0.31), residues: 293
  loop : -1.45 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  18 
 TYR   0.011   0.001   TYR D 178 
 PHE   0.010   0.001   PHE A 199 
 TRP   0.005   0.001   TRP B 129 
 HIS   0.003   0.001   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8361)
  covalent geometry    : angle       0.54358 (11440)
  SS BOND              : bond        0.00647 (    3)
  SS BOND              : angle       0.67915 (    6)
  hydrogen bonds       : bond        0.04083 (  386)
  hydrogen bonds       : angle       3.98466 ( 1092)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2327.95 seconds
wall clock time: 40 minutes 19.90 seconds (2419.90 seconds total)