Starting phenix.real_space_refine
on Thu Jul  2 15:57:55 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8hd0_34668/07_2026/8hd0_34668.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hd0_34668/07_2026/8hd0_34668.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hd0_34668/07_2026/8hd0_34668.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hd0_34668/07_2026/8hd0_34668.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8hd0_34668/07_2026/8hd0_34668.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8hd0_34668/07_2026/8hd0_34668.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hd0_34668/07_2026/8hd0_34668.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hd0_34668/07_2026/8hd0_34668.cif"
  }
  resolution = 3.11
  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=  -0.000 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      30      5.16       5
     C    5699      2.51       5
     N    1682      2.21       5
     O    1679      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9096
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1669
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 7, 'TRANS': 210}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "B"
      Number of atoms: 1670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1670
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 7, 'TRANS': 210}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "C"
      Number of atoms: 1918
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 1918
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 108}
          Link IDs: {'PTRANS': 9, 'TRANS': 289}
          Unresolved non-hydrogen bonds: 393
          Unresolved non-hydrogen angles: 505
          Unresolved non-hydrogen dihedrals: 313
          Unresolved non-hydrogen chiralities: 35
          Planarities with less than four sites: {'ASN:plan1': 6, 'GLU:plan': 11, 'ARG:plan': 8, 'ASP:plan': 14, 'GLN:plan1': 10, 'TYR:plan': 4, 'PHE:plan': 3, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 248
    Chain: "D"
      Number of atoms: 1888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 1888
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 117}
          Link IDs: {'PTRANS': 9, 'TRANS': 289}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 425
          Unresolved non-hydrogen angles: 547
          Unresolved non-hydrogen dihedrals: 337
          Unresolved non-hydrogen chiralities: 41
          Planarities with less than four sites: {'ASN:plan1': 6, 'GLU:plan': 11, 'GLN:plan1': 13, 'ARG:plan': 9, 'TYR:plan': 3, 'ASP:plan': 12, 'PHE:plan': 5, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 264
    Chain: "E"
      Number of atoms: 1889
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 380, 1869
          Classifications: {'peptide': 380}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 300}
          Link IDs: {'PTRANS': 8, 'TRANS': 371}
          Unresolved chain link angles: 8
          Unresolved non-hydrogen bonds: 1137
          Unresolved non-hydrogen angles: 1428
          Unresolved non-hydrogen dihedrals: 923
          Unresolved non-hydrogen chiralities: 85
          Planarities with less than four sites: {'GLN:plan1': 49, 'ASP:plan': 7, 'GLU:plan': 36, 'ARG:plan': 34, 'ASN:plan1': 10, 'PHE:plan': 4, 'HIS:plan': 3, 'TYR:plan': 9, 'TRP:plan': 4, 'ARG%COO:plan': 1}
          Unresolved non-hydrogen planarities: 704
      Conformer: "B"
        Number of residues, atoms: 380, 1869
          Classifications: {'peptide': 380}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 300}
          Link IDs: {'PTRANS': 8, 'TRANS': 371}
          Unresolved chain link angles: 8
          Unresolved non-hydrogen bonds: 1137
          Unresolved non-hydrogen angles: 1428
          Unresolved non-hydrogen dihedrals: 923
          Unresolved non-hydrogen chiralities: 85
          Planarities with less than four sites: {'GLN:plan1': 49, 'ASP:plan': 7, 'GLU:plan': 36, 'ARG:plan': 34, 'ASN:plan1': 10, 'PHE:plan': 4, 'HIS:plan': 3, 'TYR:plan': 9, 'TRP:plan': 4, 'ARG%COO:plan': 1}
          Unresolved non-hydrogen planarities: 704
          bond proxies already assigned to first conformer: 1844
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N  AGLU E 233 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BGLU E 233 " occ=0.50
    residue:
      pdb=" N  AARG E 237 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BARG E 237 " occ=0.50
    residue:
      pdb=" N  AARG E 262 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BARG E 262 " occ=0.50
    residue:
      pdb=" N  AVAL E 302 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BVAL E 302 " occ=0.50
  Time building chain proxies: 2.63, per 1000 atoms: 0.29
  Number of scatterers: 9096
  At special positions: 0
  Unit cell: (68.04, 91.56, 253.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P       6     15.00
     O    1679      8.00
     N    1682      7.00
     C    5699      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 528.5 milliseconds
  

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2592

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 9 sheets defined
      58.8% alpha, 8.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 50
    Processing helix  chain 'A' and resid 73 through 80
      removed outlier: 3.608A  pdb=" N   LEU A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 108
      Proline residue:  A 103  - end of helix
    Processing helix  chain 'A' and resid 110 through 125
      removed outlier: 3.857A  pdb=" N   VAL A 125 " --> pdb=" O   ALA A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 131
    Processing helix  chain 'A' and resid 134 through 138
    Processing helix  chain 'A' and resid 139 through 152
    Processing helix  chain 'A' and resid 153 through 155
      No H-bonds generated for 'chain 'A' and resid 153 through 155'
    Processing helix  chain 'A' and resid 169 through 185
    Processing helix  chain 'A' and resid 196 through 201
      removed outlier: 4.217A  pdb=" N   ILE A 200 " --> pdb=" O   ASP A 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 50
    Processing helix  chain 'B' and resid 73 through 77
    Processing helix  chain 'B' and resid 95 through 108
      Proline residue:  B 103  - end of helix
    Processing helix  chain 'B' and resid 110 through 124
    Processing helix  chain 'B' and resid 127 through 131
      removed outlier: 3.505A  pdb=" N   ALA B 131 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 138
      removed outlier: 3.604A  pdb=" N   LEU B 138 " --> pdb=" O   PRO B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 153
    Processing helix  chain 'B' and resid 169 through 185
    Processing helix  chain 'B' and resid 197 through 202
      removed outlier: 3.586A  pdb=" N   ARG B 202 " --> pdb=" O   ASN B 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 79
    Processing helix  chain 'C' and resid 80 through 107
      removed outlier: 3.635A  pdb=" N   VAL C  90 " --> pdb=" O   LEU C  86 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   LEU C  97 " --> pdb=" O   ILE C  93 " (cutoff:3.500A)
      Proline residue:  C  98  - end of helix
      removed outlier: 4.186A  pdb=" N   MET C 103 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   VAL C 104 " --> pdb=" O   VAL C 100 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   TYR C 105 " --> pdb=" O   CYS C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 130 through 141
      removed outlier: 3.887A  pdb=" N   ALA C 135 " --> pdb=" O   ASP C 131 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 156 through 165
      removed outlier: 3.856A  pdb=" N   GLY C 160 " --> pdb=" O   GLU C 156 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   GLU C 161 " --> pdb=" O   ASP C 157 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   PHE C 162 " --> pdb=" O   ALA C 158 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 189 through 194
      removed outlier: 3.609A  pdb=" N   GLY C 194 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 194 through 207
      removed outlier: 3.632A  pdb=" N   THR C 200 " --> pdb=" O   GLU C 196 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   LEU C 201 " --> pdb=" O   SER C 197 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ASP C 203 " --> pdb=" O   ASN C 199 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 225
    Processing helix  chain 'C' and resid 229 through 261
      removed outlier: 3.680A  pdb=" N   SER C 235 " --> pdb=" O   VAL C 231 " (cutoff:3.500A)
      removed outlier: 4.899A  pdb=" N   ALA C 236 " --> pdb=" O   GLY C 232 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   PHE C 247 " --> pdb=" O   VAL C 243 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ARG C 261 " --> pdb=" O   SER C 257 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 270
      removed outlier: 3.668A  pdb=" N   ILE C 265 " --> pdb=" O   ARG C 261 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 279 through 300
      removed outlier: 3.511A  pdb=" N   GLY C 285 " --> pdb=" O   PRO C 281 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   LEU C 289 " --> pdb=" O   GLY C 285 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU C 296 " --> pdb=" O   SER C 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 320
      removed outlier: 3.925A  pdb=" N   SER C 310 " --> pdb=" O   LEU C 306 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   ALA C 311 " --> pdb=" O   ARG C 307 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   GLN C 317 " --> pdb=" O   ALA C 313 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   VAL C 318 " --> pdb=" O   GLU C 314 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 329 through 355
      removed outlier: 4.134A  pdb=" N   LEU C 335 " --> pdb=" O   ASP C 331 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 64 through 79
    Processing helix  chain 'D' and resid 80 through 116
      removed outlier: 4.159A  pdb=" N   LEU D  97 " --> pdb=" O   ILE D  93 " (cutoff:3.500A)
      Proline residue:  D  98  - end of helix
      removed outlier: 3.641A  pdb=" N   TYR D 116 " --> pdb=" O   ALA D 112 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 130 through 141
    Processing helix  chain 'D' and resid 156 through 164
      removed outlier: 3.573A  pdb=" N   GLY D 160 " --> pdb=" O   GLU D 156 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   GLU D 161 " --> pdb=" O   ASP D 157 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   PHE D 162 " --> pdb=" O   ALA D 158 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 189 through 194
      removed outlier: 3.912A  pdb=" N   GLY D 194 " --> pdb=" O   LEU D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 194 through 207
      removed outlier: 5.036A  pdb=" N   THR D 200 " --> pdb=" O   GLU D 196 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   LEU D 201 " --> pdb=" O   SER D 197 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 219 through 261
      removed outlier: 4.306A  pdb=" N   SER D 235 " --> pdb=" O   VAL D 231 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 264 through 271
      removed outlier: 4.333A  pdb=" N   GLN D 268 " --> pdb=" O   SER D 264 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ILE D 271 " --> pdb=" O   VAL D 267 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 274 through 319
      removed outlier: 3.512A  pdb=" N   ARG D 280 " --> pdb=" O   GLY D 276 " (cutoff:3.500A)
      Proline residue:  D 281  - end of helix
      removed outlier: 3.789A  pdb=" N   LEU D 289 " --> pdb=" O   GLY D 285 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   SER D 310 " --> pdb=" O   LEU D 306 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   ALA D 311 " --> pdb=" O   ARG D 307 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   VAL D 312 " --> pdb=" O   LEU D 308 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 329 through 359
      removed outlier: 3.548A  pdb=" N   ARG D 357 " --> pdb=" O   VAL D 353 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   HIS D 358 " --> pdb=" O   GLN D 354 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 41 through 51
    Processing helix  chain 'E' and resid 52 through 123
      removed outlier: 4.657A  pdb=" N   GLN E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 144 through 150
    Processing helix  chain 'E' and resid 152 through 217
    Processing helix  chain 'E' and resid 221 through 247
    Processing helix  chain 'E' and resid 248 through 271
      removed outlier: 4.129A  pdb=" N   GLU E 252 " --> pdb=" O   LYS E 248 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 278 through 286
    Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 25
      removed outlier: 5.436A  pdb=" N   GLN A  19 " --> pdb=" O   LYS A   9 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   LYS A   9 " --> pdb=" O   GLN A  19 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   PHE A  23 " --> pdb=" O   GLU A   5 " (cutoff:3.500A)
      removed outlier: 5.151A  pdb=" N   GLU A   5 " --> pdb=" O   PHE A  23 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   MET A  25 " --> pdb=" O   ARG A   3 " (cutoff:3.500A)
      removed outlier: 5.354A  pdb=" N   ARG A   3 " --> pdb=" O   MET A  25 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   VAL A   7 " --> pdb=" O   ALA A  56 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ALA A  56 " --> pdb=" O   VAL A   7 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 84
      removed outlier: 6.465A  pdb=" N   LEU A 159 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
      removed outlier: 7.458A  pdb=" N   ALA A 193 " --> pdb=" O   LEU A 159 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ALA A 161 " --> pdb=" O   ALA A 193 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   ALA A  31 " --> pdb=" O   MET A 192 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   PHE A  32 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   LEU A 210 " --> pdb=" O   PHE A  32 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   THR A  34 " --> pdb=" O   LEU A 210 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 15 through 25
      removed outlier: 6.492A  pdb=" N   ALA B  17 " --> pdb=" O   ALA B  10 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   ALA B  10 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   GLN B  19 " --> pdb=" O   SER B   8 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   SER B   8 " --> pdb=" O   GLN B  19 " (cutoff:3.500A)
      removed outlier: 5.415A  pdb=" N   VAL B  21 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   VAL B   7 " --> pdb=" O   ALA B  56 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ALA B  56 " --> pdb=" O   VAL B   7 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 84
      removed outlier: 6.401A  pdb=" N   GLY B  82 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   ASP B 162 " --> pdb=" O   GLY B  82 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   ILE B  84 " --> pdb=" O   ASP B 162 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   LEU B 159 " --> pdb=" O   LEU B 191 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   ALA B 193 " --> pdb=" O   LEU B 159 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ALA B 161 " --> pdb=" O   ALA B 193 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA B  31 " --> pdb=" O   VAL B 190 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 150 through 151
    Processing sheet with id=AA6, first strand: chain 'D' and resid 151 through 152
    Processing sheet with id=AA7, first strand: chain 'E' and resid 313 through 315
      removed outlier: 4.487A  pdb=" N   GLN E 315 " --> pdb=" O   LEU E 318 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LEU E 318 " --> pdb=" O   GLN E 315 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 322 through 326
      removed outlier: 4.408A  pdb=" N   ILE E 404 " --> pdb=" O   VAL E 411 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 340 through 344
      removed outlier: 4.711A  pdb=" N   VAL E 341 " --> pdb=" O   GLU E 357 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   GLU E 357 " --> pdb=" O   VAL E 341 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL E 354 " --> pdb=" O   TYR E 366 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   VAL E 356 " --> pdb=" O   SER E 364 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   SER E 364 " --> pdb=" O   VAL E 356 " (cutoff:3.500A)

    628 hydrogen bonds defined for protein.
    1839 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: 1.57

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2854
        1.33 -     1.45: 1165
        1.45 -     1.57: 5142
        1.57 -     1.69: 10
        1.69 -     1.81: 52
  Bond restraints: 9223
  Sorted by residual:
  bond pdb=" N   VAL C 185 "
       pdb=" CA  VAL C 185 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.037 1.19e-02 7.06e+03 9.58e+00
  bond pdb=" N   VAL C 186 "
       pdb=" CA  VAL C 186 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.037 1.23e-02 6.61e+03 9.06e+00
  bond pdb=" N   VAL C 183 "
       pdb=" CA  VAL C 183 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.72e+00
  bond pdb=" N   ILE C 121 "
       pdb=" CA  ILE C 121 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 8.02e+00
  bond pdb=" N   ILE C 211 "
       pdb=" CA  ILE C 211 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.96e+00
  ... (remaining 9218 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.48: 12395
        2.48 -     4.95: 214
        4.95 -     7.43: 23
        7.43 -     9.90: 3
        9.90 -    12.38: 2
  Bond angle restraints: 12637
  Sorted by residual:
  angle pdb=" PB  ATP B 301 "
        pdb=" O3B ATP B 301 "
        pdb=" PG  ATP B 301 "
      ideal   model   delta    sigma   weight residual
     139.87  129.08   10.79 1.00e+00 1.00e+00 1.16e+02
  angle pdb=" PB  ATP A 301 "
        pdb=" O3B ATP A 301 "
        pdb=" PG  ATP A 301 "
      ideal   model   delta    sigma   weight residual
     139.87  130.49    9.38 1.00e+00 1.00e+00 8.80e+01
  angle pdb=" N   ALA C 225 "
        pdb=" CA  ALA C 225 "
        pdb=" C   ALA C 225 "
      ideal   model   delta    sigma   weight residual
     114.62  108.03    6.59 1.14e+00 7.69e-01 3.34e+01
  angle pdb=" PA  ATP B 301 "
        pdb=" O3A ATP B 301 "
        pdb=" PB  ATP B 301 "
      ideal   model   delta    sigma   weight residual
     136.83  131.79    5.04 1.00e+00 1.00e+00 2.54e+01
  angle pdb=" N   VAL C 100 "
        pdb=" CA  VAL C 100 "
        pdb=" C   VAL C 100 "
      ideal   model   delta    sigma   weight residual
     112.96  108.55    4.41 1.00e+00 1.00e+00 1.95e+01
  ... (remaining 12632 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.38: 4814
       16.38 -    32.76: 391
       32.76 -    49.14: 137
       49.14 -    65.52: 30
       65.52 -    81.90: 4
  Dihedral angle restraints: 5376
    sinusoidal: 1352
      harmonic: 4024
  Sorted by residual:
  dihedral pdb=" CA  GLU E 114 "
           pdb=" C   GLU E 114 "
           pdb=" N   ARG E 115 "
           pdb=" CA  ARG E 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.16   26.84     0      5.00e+00 4.00e-02 2.88e+01
  dihedral pdb=" CA  HIS A 195 "
           pdb=" C   HIS A 195 "
           pdb=" N   ASP A 196 "
           pdb=" CA  ASP A 196 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.77   22.23     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  SER D 264 "
           pdb=" C   SER D 264 "
           pdb=" N   ILE D 265 "
           pdb=" CA  ILE D 265 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.84   22.16     0      5.00e+00 4.00e-02 1.96e+01
  ... (remaining 5373 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1355
       0.066 -    0.131: 173
       0.131 -    0.197: 28
       0.197 -    0.262: 4
       0.262 -    0.328: 2
  Chirality restraints: 1562
  Sorted by residual:
  chirality pdb=" CB  THR C 360 "
            pdb=" CA  THR C 360 "
            pdb=" OG1 THR C 360 "
            pdb=" CG2 THR C 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.22    0.33 2.00e-01 2.50e+01 2.69e+00
  chirality pdb=" CB  VAL B  96 "
            pdb=" CA  VAL B  96 "
            pdb=" CG1 VAL B  96 "
            pdb=" CG2 VAL B  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CA  LEU C 198 "
            pdb=" N   LEU C 198 "
            pdb=" C   LEU C 198 "
            pdb=" CB  LEU C 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 1559 not shown)

  Planarity restraints: 1674
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS E 110 "    0.022 2.00e-02 2.50e+03   4.44e-02 1.97e+01
        pdb=" C   LYS E 110 "   -0.077 2.00e-02 2.50e+03
        pdb=" O   LYS E 110 "    0.028 2.00e-02 2.50e+03
        pdb=" N   ALA E 111 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG D 280 "    0.060 5.00e-02 4.00e+02   9.00e-02 1.29e+01
        pdb=" N   PRO D 281 "   -0.156 5.00e-02 4.00e+02
        pdb=" CA  PRO D 281 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO D 281 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA E 104 "   -0.015 2.00e-02 2.50e+03   2.97e-02 8.84e+00
        pdb=" C   ALA E 104 "    0.051 2.00e-02 2.50e+03
        pdb=" O   ALA E 104 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LYS E 105 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1671 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 104
        2.64 -     3.21: 8615
        3.21 -     3.77: 13968
        3.77 -     4.34: 17617
        4.34 -     4.90: 29660
  Nonbonded interactions: 69964
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 139 "
            pdb=" OE1 GLU A 142 "
     model   vdw
     2.075 3.040
  nonbonded pdb=" O   ASP A 169 "
            pdb=" OG  SER A 173 "
     model   vdw
     2.117 3.040
  nonbonded pdb=" NH2 ARG A  79 "
            pdb=" O   GLY D 272 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" O   ASP C  76 "
            pdb=" OG  SER C  79 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OH  TYR B  11 "
            pdb=" OG1 THR B  43 "
     model   vdw
     2.244 3.040
  ... (remaining 69959 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 13 through 196 or (resid 197 through 198 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 199 through 301))
  selection = (chain 'B' and (resid 1 through 67 or (resid 68 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 69 or (resid 70 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 71 through 301))
}
ncs_group {
  reference = (chain 'C' and ((resid 63 through 65 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 66 through 74 or (resid 75 through 76 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 77 through 220 or (resid 221 thro \ 
ugh 223 and (name N or name CA or name C or name O or name CB )) or resid 224 th \ 
rough 226 or (resid 227 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 228 through 229 or (resid 230 through 231 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 232 or (resid 233 through 234 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 235 through 307 or (resid  \ 
308 through 319 and (name N or name CA or name C or name O or name CB )) or (res \ 
id 320 through 326 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 327 through 331 or (resid 332 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 333 through 353 or (resid 354 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 355 through 359 or (resid 360 through 361 a \ 
nd (name N or name CA or name C or name O or name CB ))))
  selection = (chain 'D' and (resid 63 through 75 or (resid 76 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 77 through 105 or (resid 106 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 107 through 108 or (resid 109  \ 
through 116 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 
7 through 218 or (resid 219 through 223 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 224 through 233 or (resid 234 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 235 through 256 or (resid 257 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 258 through 262 or (re \ 
sid 263 and (name N or name CA or name C or name O or name CB )) or resid 264 th \ 
rough 301 or (resid 302 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 303 through 333 or (resid 334 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 335 through 361))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             17.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     10.800
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
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      :  0.007   0.063   9223  Z= 0.338
  Angle     :  0.798  12.378  12637  Z= 0.487
  Chirality :  0.050   0.328   1562
  Planarity :  0.005   0.090   1674
  Dihedral  : 15.158  81.897   2784
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  :  9.62 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 27.36 %
    Favored  : 71.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.94 (0.23), residues: 1416
  helix:  0.81 (0.19), residues: 766
  sheet: -2.27 (0.51), residues: 68
  loop : -2.46 (0.25), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 233 
 TYR   0.008   0.001   TYR C  68 
 PHE   0.018   0.002   PHE B  23 
 TRP   0.012   0.002   TRP D 345 
 HIS   0.006   0.001   HIS A 195 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00667 /  0.34 ( 9223)
  covalent geometry    : angle       0.79838 /  0.49 (12637)
  hydrogen bonds       : bond        0.16783 / 10.95 (  628)
  hydrogen bonds       : angle       6.80848 /  4.89 ( 1839)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 133
  time to evaluate  : 0.355 
Fit side-chains
REVERT: A   71 ASN cc_start: 0.8147 (m-40) cc_final: 0.7845 (t0)
REVERT: C  306 LEU cc_start: 0.6695 (mt) cc_final: 0.6360 (pp)
  outliers start: 9
  outliers final: 2
  residues processed: 139
  average time/residue: 0.1454
  time to fit residues: 25.6759
Evaluate side-chains
  104 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 102
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  221 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    0.1980
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:   50.0000
   chunk 124 optimal weight:   20.0000
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:   30.0000
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    0.8980
   chunk 55 optimal weight:    8.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  71 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.223991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.184887 restraints weight = 30760.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.4109 rms_B_bonded: 3.78
r_work: 0.3289 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9223  Z= 0.229
  Angle     :  0.693  11.929  12637  Z= 0.355
  Chirality :  0.043   0.219   1562
  Planarity :  0.005   0.060   1674
  Dihedral  :  5.229  50.300   1487
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  8.48 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  7.33 %
    Allowed  : 21.82 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.58 (0.22), residues: 1416
  helix:  1.18 (0.19), residues: 765
  sheet: -1.58 (0.59), residues: 60
  loop : -2.48 (0.24), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  53 
 TYR   0.022   0.002   TYR C 105 
 PHE   0.014   0.002   PHE A  23 
 TRP   0.016   0.002   TRP A  60 
 HIS   0.004   0.001   HIS B 214 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00543 /  0.23 ( 9223)
  covalent geometry    : angle       0.69334 /  0.36 (12637)
  hydrogen bonds       : bond        0.06094 /  4.08 (  628)
  hydrogen bonds       : angle       5.40129 /  3.95 ( 1839)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 119
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A   71 ASN cc_start: 0.8524 (m-40) cc_final: 0.7758 (t0)
REVERT: A   84 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7790 (pt)
REVERT: B   53 ARG cc_start: 0.8823 (ttm170) cc_final: 0.8418 (mtm180)
REVERT: C   68 TYR cc_start: 0.7929 (t80) cc_final: 0.7699 (t80)
REVERT: C  319 PHE cc_start: 0.6244 (t80) cc_final: 0.5946 (t80)
REVERT: D   79 SER cc_start: 0.8537 (p) cc_final: 0.8319 (p)
REVERT: D  241 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7466 (mp)
REVERT: D  268 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.7999 (tt0)
REVERT: D  302 GLU cc_start: 0.6523 (tm-30) cc_final: 0.6175 (tp30)
  outliers start: 45
  outliers final: 25
  residues processed: 154
  average time/residue: 0.1091
  time to fit residues: 22.6311
Evaluate side-chains
  136 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  261 ARG
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain C residue  355 HIS
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  265 ILE
Chi-restraints excluded: chain D residue  266 ASN
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 85 optimal weight:   20.0000
   chunk 108 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 76 optimal weight:    6.9990
   chunk 10 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 25 optimal weight:    0.1980
   chunk 78 optimal weight:   30.0000
   chunk 119 optimal weight:    5.9990
   chunk 35 optimal weight:    0.3980
   chunk 109 optimal weight:   20.0000
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.221336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.182610 restraints weight = 33256.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.4083 rms_B_bonded: 3.85
r_work: 0.3278 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3246
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3246 r_free = 0.3246    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3246 r_free = 0.3246    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3246
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9223  Z= 0.229
  Angle     :  0.671  11.640  12637  Z= 0.342
  Chirality :  0.043   0.209   1562
  Planarity :  0.004   0.056   1674
  Dihedral  :  5.043  61.349   1485
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  7.55 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  7.17 %
    Allowed  : 21.99 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.33 (0.23), residues: 1416
  helix:  1.34 (0.19), residues: 769
  sheet: -1.23 (0.61), residues: 60
  loop : -2.36 (0.24), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 262 
 TYR   0.015   0.001   TYR C 105 
 PHE   0.019   0.002   PHE C 247 
 TRP   0.016   0.002   TRP D 345 
 HIS   0.005   0.002   HIS B 214 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00549 /  0.23 ( 9223)
  covalent geometry    : angle       0.67117 /  0.34 (12637)
  hydrogen bonds       : bond        0.05775 /  3.90 (  628)
  hydrogen bonds       : angle       5.11519 /  3.75 ( 1839)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 112
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A   83 MET cc_start: 0.8627 (ptt) cc_final: 0.7770 (ttt)
REVERT: A   84 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7812 (mp)
REVERT: A  195 HIS cc_start: 0.8417 (OUTLIER) cc_final: 0.8008 (p-80)
REVERT: A  208 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8365 (mt)
REVERT: B  207 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7636 (tmm)
REVERT: C   68 TYR cc_start: 0.7991 (t80) cc_final: 0.7717 (t80)
REVERT: C  319 PHE cc_start: 0.6053 (t80) cc_final: 0.5662 (t80)
REVERT: C  355 HIS cc_start: 0.6478 (OUTLIER) cc_final: 0.6200 (t-90)
REVERT: D   79 SER cc_start: 0.8483 (p) cc_final: 0.8247 (p)
REVERT: D  241 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7471 (mp)
REVERT: D  268 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.7898 (tt0)
  outliers start: 44
  outliers final: 26
  residues processed: 146
  average time/residue: 0.1023
  time to fit residues: 20.4471
Evaluate side-chains
  145 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   30 MET
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  113 ASP
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  261 ARG
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain C residue  355 HIS
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  266 ASN
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 84 optimal weight:    8.9990
   chunk 86 optimal weight:   20.0000
   chunk 54 optimal weight:   20.0000
   chunk 70 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 23 optimal weight:    0.4980
   chunk 9 optimal weight:    0.0980
   chunk 101 optimal weight:    8.9990
   chunk 129 optimal weight:   30.0000
   chunk 121 optimal weight:   50.0000
   chunk 117 optimal weight:   40.0000
   overall best weight:    2.4984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 216 HIS
** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 109 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.214795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.179111 restraints weight = 37562.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.4046 rms_B_bonded: 2.99
r_work: 0.3288 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3269
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3269
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.3424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.015   0.124   9223  Z= 0.586
  Angle     :  1.020  12.754  12637  Z= 0.510
  Chirality :  0.062   0.527   1562
  Planarity :  0.006   0.064   1674
  Dihedral  :  5.727  73.595   1485
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  9.19 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  9.93 %
    Allowed  : 20.68 %
    Favored  : 69.38 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.22), residues: 1416
  helix:  0.68 (0.18), residues: 769
  sheet: -1.78 (0.58), residues: 60
  loop : -2.59 (0.24), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 117 
 TYR   0.012   0.003   TYR B 205 
 PHE   0.029   0.004   PHE C 247 
 TRP   0.028   0.005   TRP D 345 
 HIS   0.012   0.003   HIS B  89 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01475 /  0.59 ( 9223)
  covalent geometry    : angle       1.02035 /  0.51 (12637)
  hydrogen bonds       : bond        0.08354 /  5.75 (  628)
  hydrogen bonds       : angle       5.44933 /  3.96 ( 1839)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 109
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8056 (tp30)
REVERT: A   83 MET cc_start: 0.8637 (ptt) cc_final: 0.7782 (ttt)
REVERT: A  155 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8017 (pttt)
REVERT: A  195 HIS cc_start: 0.9025 (OUTLIER) cc_final: 0.8553 (p-80)
REVERT: A  208 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8452 (mt)
REVERT: B  203 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8425 (mmt90)
REVERT: B  207 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7596 (tmm)
REVERT: C  269 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8319 (tttp)
REVERT: C  319 PHE cc_start: 0.6188 (t80) cc_final: 0.5840 (t80)
REVERT: D   79 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8399 (p)
REVERT: D  241 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7249 (mp)
REVERT: D  268 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8072 (tt0)
REVERT: D  307 ARG cc_start: 0.8188 (tpp-160) cc_final: 0.7841 (tpp-160)
  outliers start: 61
  outliers final: 32
  residues processed: 159
  average time/residue: 0.1044
  time to fit residues: 22.7808
Evaluate side-chains
  145 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 103
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  155 LYS
Chi-restraints excluded: chain A residue  169 ASP
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   30 MET
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  203 ARG
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  269 LYS
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  297 SER
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  355 HIS
Chi-restraints excluded: chain D residue   79 SER
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  266 ASN
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 52 optimal weight:   30.0000
   chunk 39 optimal weight:    0.6980
   chunk 99 optimal weight:    0.5980
   chunk 14 optimal weight:    0.3980
   chunk 108 optimal weight:    9.9990
   chunk 77 optimal weight:   30.0000
   chunk 57 optimal weight:    0.0060
   chunk 12 optimal weight:    0.5980
   chunk 49 optimal weight:   30.0000
   chunk 92 optimal weight:    0.0980
   chunk 115 optimal weight:   50.0000
   overall best weight:    0.3396

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 195 HIS
** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.222236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.187593 restraints weight = 36241.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.4141 rms_B_bonded: 3.07
r_work: 0.3396 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3372
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3372
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.3483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9223  Z= 0.145
  Angle     :  0.599  12.221  12637  Z= 0.309
  Chirality :  0.041   0.188   1562
  Planarity :  0.004   0.054   1674
  Dihedral  :  4.860  56.650   1485
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  6.84 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 24.43 %
    Favored  : 70.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.23), residues: 1416
  helix:  1.36 (0.19), residues: 779
  sheet: -0.84 (0.67), residues: 50
  loop : -2.34 (0.24), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  78 
 TYR   0.006   0.001   TYR B 205 
 PHE   0.023   0.001   PHE C 247 
 TRP   0.012   0.001   TRP D 345 
 HIS   0.006   0.001   HIS C 358 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.15 ( 9223)
  covalent geometry    : angle       0.59887 /  0.31 (12637)
  hydrogen bonds       : bond        0.04905 /  3.28 (  628)
  hydrogen bonds       : angle       4.91432 /  3.59 ( 1839)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 99
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A   83 MET cc_start: 0.8563 (ptt) cc_final: 0.7706 (ttt)
REVERT: A  183 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7500 (t80)
REVERT: B   87 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7632 (m-30)
REVERT: C   68 TYR cc_start: 0.8020 (t80) cc_final: 0.7706 (t80)
REVERT: C   95 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8540 (tt)
REVERT: C  355 HIS cc_start: 0.6495 (OUTLIER) cc_final: 0.6191 (t-90)
REVERT: D  241 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7486 (mp)
REVERT: D  268 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7851 (tt0)
REVERT: D  307 ARG cc_start: 0.7929 (tpp-160) cc_final: 0.7714 (tpp-160)
REVERT: D  330 PHE cc_start: 0.4776 (OUTLIER) cc_final: 0.3665 (t80)
REVERT: D  352 THR cc_start: 0.7792 (m) cc_final: 0.7589 (m)
  outliers start: 31
  outliers final: 19
  residues processed: 120
  average time/residue: 0.1132
  time to fit residues: 18.1462
Evaluate side-chains
  123 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 97
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   87 ASP
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  355 HIS
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  330 PHE
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 23 optimal weight:    0.3980
   chunk 82 optimal weight:    0.0770
   chunk 26 optimal weight:    0.0970
   chunk 38 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 25 optimal weight:    0.1980
   chunk 71 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 123 optimal weight:   50.0000
   chunk 15 optimal weight:    0.3980
   overall best weight:    0.2336

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 184 ASN
** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.225437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.188991 restraints weight = 33472.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.4148 rms_B_bonded: 3.36
r_work: 0.3397 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3379
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3379 r_free = 0.3379    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3379 r_free = 0.3379    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3379
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.3753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9223  Z= 0.120
  Angle     :  0.555  12.488  12637  Z= 0.284
  Chirality :  0.039   0.195   1562
  Planarity :  0.003   0.054   1674
  Dihedral  :  4.370  44.519   1485
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  6.55 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 23.29 %
    Favored  : 72.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.23), residues: 1416
  helix:  1.80 (0.19), residues: 781
  sheet: -1.24 (0.65), residues: 63
  loop : -2.15 (0.25), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 262 
 TYR   0.004   0.000   TYR C 102 
 PHE   0.019   0.001   PHE C 247 
 TRP   0.010   0.001   TRP D 345 
 HIS   0.006   0.001   HIS C 358 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.12 ( 9223)
  covalent geometry    : angle       0.55458 /  0.28 (12637)
  hydrogen bonds       : bond        0.04260 /  2.84 (  628)
  hydrogen bonds       : angle       4.59301 /  3.36 ( 1839)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A   90 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8269 (pp)
REVERT: C  355 HIS cc_start: 0.6275 (OUTLIER) cc_final: 0.5942 (t-90)
  outliers start: 27
  outliers final: 18
  residues processed: 117
  average time/residue: 0.1210
  time to fit residues: 18.7272
Evaluate side-chains
  120 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  195 HIS
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  355 HIS
Chi-restraints excluded: chain D residue  237 MET
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  334 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 45 optimal weight:    0.0170
   chunk 101 optimal weight:   50.0000
   chunk 118 optimal weight:    2.9990
   chunk 110 optimal weight:   20.0000
   chunk 100 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 133 optimal weight:   50.0000
   chunk 34 optimal weight:    0.8980
   chunk 52 optimal weight:    8.9990
   chunk 121 optimal weight:   50.0000
   overall best weight:    1.1220

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.218984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.182571 restraints weight = 37627.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.4091 rms_B_bonded: 3.00
r_work: 0.3345 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3319
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3319 r_free = 0.3319    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3319 r_free = 0.3319    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3319
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.3849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061   9223  Z= 0.289
  Angle     :  0.724  12.038  12637  Z= 0.363
  Chirality :  0.046   0.242   1562
  Planarity :  0.004   0.058   1674
  Dihedral  :  4.872  64.379   1485
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  7.19 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 23.94 %
    Favored  : 70.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.23), residues: 1416
  helix:  1.62 (0.19), residues: 775
  sheet: -1.56 (0.58), residues: 72
  loop : -2.28 (0.25), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 261 
 TYR   0.009   0.001   TYR B 205 
 PHE   0.018   0.002   PHE A  23 
 TRP   0.017   0.003   TRP D 345 
 HIS   0.015   0.002   HIS A 195 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00721 /  0.29 ( 9223)
  covalent geometry    : angle       0.72387 /  0.36 (12637)
  hydrogen bonds       : bond        0.05867 /  4.00 (  628)
  hydrogen bonds       : angle       4.76328 /  3.46 ( 1839)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 101
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A   90 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8641 (pp)
REVERT: A  208 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8385 (mt)
REVERT: C   95 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8552 (tt)
REVERT: C  355 HIS cc_start: 0.6605 (OUTLIER) cc_final: 0.6234 (t-90)
  outliers start: 36
  outliers final: 25
  residues processed: 129
  average time/residue: 0.1091
  time to fit residues: 19.1358
Evaluate side-chains
  131 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 102
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  355 HIS
Chi-restraints excluded: chain D residue  237 MET
Chi-restraints excluded: chain D residue  266 ASN
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 117 optimal weight:    7.9990
   chunk 38 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 28 optimal weight:    0.4980
   chunk 100 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0970
   chunk 4 optimal weight:    0.2980
   chunk 51 optimal weight:   20.0000
   overall best weight:    0.4178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 214 HIS
B 216 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.222432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.170683 restraints weight = 30825.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3910 rms_B_bonded: 10.16
r_work: 0.3025 rms_B_bonded: 6.47 restraints_weight: 2.0000
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2984
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2984 r_free = 0.2984    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2984 r_free = 0.2984    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2984
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.3972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9223  Z= 0.145
  Angle     :  0.584  12.286  12637  Z= 0.298
  Chirality :  0.040   0.209   1562
  Planarity :  0.003   0.055   1674
  Dihedral  :  4.535  53.808   1485
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  6.91 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 23.94 %
    Favored  : 70.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.23), residues: 1416
  helix:  1.82 (0.19), residues: 775
  sheet: -1.09 (0.65), residues: 62
  loop : -2.19 (0.25), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 261 
 TYR   0.004   0.001   TYR C 102 
 PHE   0.018   0.001   PHE C 247 
 TRP   0.013   0.001   TRP D 345 
 HIS   0.008   0.001   HIS A 195 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.15 ( 9223)
  covalent geometry    : angle       0.58443 /  0.30 (12637)
  hydrogen bonds       : bond        0.04622 /  3.09 (  628)
  hydrogen bonds       : angle       4.56694 /  3.33 ( 1839)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 96
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A   90 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8360 (pp)
REVERT: A  195 HIS cc_start: 0.7871 (OUTLIER) cc_final: 0.7494 (p90)
REVERT: C   95 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8383 (tt)
REVERT: C  306 LEU cc_start: 0.6557 (mt) cc_final: 0.5670 (pp)
REVERT: C  355 HIS cc_start: 0.6090 (OUTLIER) cc_final: 0.5872 (t-90)
  outliers start: 33
  outliers final: 26
  residues processed: 120
  average time/residue: 0.0988
  time to fit residues: 16.0510
Evaluate side-chains
  125 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 95
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  195 HIS
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  355 HIS
Chi-restraints excluded: chain D residue  237 MET
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 43 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0980
   chunk 72 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 111 optimal weight:    5.9990
   chunk 119 optimal weight:    5.9990
   chunk 14 optimal weight:    0.4980
   chunk 78 optimal weight:   30.0000
   overall best weight:    0.5180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 216 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.221810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.185622 restraints weight = 42355.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.4118 rms_B_bonded: 3.05
r_work: 0.3374 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3340
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3340 r_free = 0.3340    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3340 r_free = 0.3340    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3340
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.4185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9223  Z= 0.162
  Angle     :  0.606  12.117  12637  Z= 0.306
  Chirality :  0.041   0.210   1562
  Planarity :  0.004   0.057   1674
  Dihedral  :  4.458  55.527   1485
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  6.91 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 23.78 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.32 (0.23), residues: 1416
  helix:  1.90 (0.19), residues: 781
  sheet: -1.65 (0.57), residues: 80
  loop : -2.09 (0.25), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 261 
 TYR   0.005   0.001   TYR C 102 
 PHE   0.016   0.001   PHE C 247 
 TRP   0.013   0.001   TRP D 345 
 HIS   0.010   0.001   HIS A 195 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00377 /  0.16 ( 9223)
  covalent geometry    : angle       0.60624 /  0.31 (12637)
  hydrogen bonds       : bond        0.04737 /  3.19 (  628)
  hydrogen bonds       : angle       4.44879 /  3.24 ( 1839)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 100
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A   83 MET cc_start: 0.8531 (ptt) cc_final: 0.7611 (ttt)
REVERT: A   90 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8447 (pp)
REVERT: A  183 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7574 (t80)
REVERT: C   95 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8521 (tt)
REVERT: C  306 LEU cc_start: 0.6674 (mt) cc_final: 0.5699 (pp)
REVERT: C  354 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7748 (tm-30)
REVERT: C  355 HIS cc_start: 0.6374 (OUTLIER) cc_final: 0.5962 (t-90)
  outliers start: 33
  outliers final: 26
  residues processed: 125
  average time/residue: 0.1086
  time to fit residues: 18.3652
Evaluate side-chains
  132 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  195 HIS
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  355 HIS
Chi-restraints excluded: chain D residue  237 MET
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 95 optimal weight:    3.9990
   chunk 100 optimal weight:    8.9990
   chunk 78 optimal weight:   30.0000
   chunk 68 optimal weight:    0.9980
   chunk 50 optimal weight:   50.0000
   chunk 104 optimal weight:    7.9990
   chunk 116 optimal weight:    8.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    1.7584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 266 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.216614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.177422 restraints weight = 36962.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.4022 rms_B_bonded: 3.70
r_work: 0.3222 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3199
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3199
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.4325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.091   9223  Z= 0.417
  Angle     :  0.859  13.836  12637  Z= 0.426
  Chirality :  0.052   0.334   1562
  Planarity :  0.005   0.061   1674
  Dihedral  :  4.996  68.069   1483
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  7.91 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 23.78 %
    Favored  : 70.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -0.19 (0.23), residues: 1416
  helix:  1.47 (0.19), residues: 779
  sheet: -1.70 (0.58), residues: 73
  loop : -2.32 (0.25), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  53 
 TYR   0.010   0.002   TYR B 205 
 PHE   0.022   0.003   PHE C 291 
 TRP   0.020   0.004   TRP D 345 
 HIS   0.015   0.003   HIS A 195 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01050 /  0.42 ( 9223)
  covalent geometry    : angle       0.85857 /  0.43 (12637)
  hydrogen bonds       : bond        0.06821 /  4.68 (  628)
  hydrogen bonds       : angle       4.76008 /  3.43 ( 1839)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 102
  time to evaluate  : 0.419 
Fit side-chains
REVERT: B  203 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7989 (mtt90)
REVERT: B  207 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7770 (tmm)
REVERT: C   95 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8648 (tt)
  outliers start: 35
  outliers final: 26
  residues processed: 129
  average time/residue: 0.1038
  time to fit residues: 18.2763
Evaluate side-chains
  132 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 103
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  203 ARG
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  297 SER
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  355 HIS
Chi-restraints excluded: chain D residue  237 MET
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  266 ASN
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 81 optimal weight:    8.9990
   chunk 102 optimal weight:   30.0000
   chunk 49 optimal weight:   30.0000
   chunk 12 optimal weight:    0.2980
   chunk 82 optimal weight:   20.0000
   chunk 34 optimal weight:    0.7980
   chunk 126 optimal weight:   40.0000
   chunk 64 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 266 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.221812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.184359 restraints weight = 36145.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.4099 rms_B_bonded: 3.44
r_work: 0.3367 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3339
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3339 r_free = 0.3339    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3339 r_free = 0.3339    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3339
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.4374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9223  Z= 0.152
  Angle     :  0.600  12.503  12637  Z= 0.305
  Chirality :  0.041   0.212   1562
  Planarity :  0.004   0.055   1674
  Dihedral  :  4.460  55.974   1483
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  6.41 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 25.73 %
    Favored  : 70.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.23), residues: 1416
  helix:  1.86 (0.19), residues: 779
  sheet: -1.83 (0.53), residues: 90
  loop : -2.10 (0.26), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  53 
 TYR   0.004   0.001   TYR C 102 
 PHE   0.017   0.001   PHE C 247 
 TRP   0.014   0.001   TRP D 345 
 HIS   0.007   0.001   HIS A 195 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.15 ( 9223)
  covalent geometry    : angle       0.60036 /  0.31 (12637)
  hydrogen bonds       : bond        0.04648 /  3.11 (  628)
  hydrogen bonds       : angle       4.43241 /  3.22 ( 1839)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2968.06 seconds
wall clock time: 51 minutes 28.12 seconds (3088.12 seconds total)