Starting phenix.real_space_refine
on Wed Jun 11 00:02:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7z2c_14461/06_2025/7z2c_14461.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7z2c_14461/06_2025/7z2c_14461.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7z2c_14461/06_2025/7z2c_14461.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7z2c_14461/06_2025/7z2c_14461.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7z2c_14461/06_2025/7z2c_14461.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7z2c_14461/06_2025/7z2c_14461.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.008
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: 7
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      65      5.16       5
     C    5940      2.51       5
     N    1637      2.21       5
     O    1833      1.98       5
     H    2554      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 12037
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "K"
      Number of atoms: 5287
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 347, 5287
          Classifications: {'peptide': 347}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 338}
    Chain: "A"
      Number of atoms: 3342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 428, 3342
          Classifications: {'peptide': 428}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "H"
      Number of atoms: 3342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3342
          Classifications: {'peptide': 426}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "H"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'G2P': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.26, per 1000 atoms: 0.52
  Number of scatterers: 12037
  At special positions: 0
  Unit cell: (111.3, 109.2, 78.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      65     16.00
     P       6     15.00
     Mg      2     11.99
     O    1833      8.00
     N    1637      7.00
     C    5940      6.00
     H    2554      1.00
    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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.02
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2236

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 10 sheets defined
      52.1% alpha, 22.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.16
  Creating SS restraints...
    Processing helix  chain 'K' and resid 16 through 22
    Processing helix  chain 'K' and resid 46 through 53
    Processing helix  chain 'K' and resid 70 through 77
    Processing helix  chain 'K' and resid 79 through 88
    Processing helix  chain 'K' and resid 103 through 109
    Processing helix  chain 'K' and resid 115 through 133
      removed outlier: 3.559A  pdb=" N   MET K 120 " --> pdb=" O   GLY K 116 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 157 through 160
    Processing helix  chain 'K' and resid 185 through 198
      removed outlier: 3.840A  pdb=" N   ARG K 198 " --> pdb=" O   HIS K 194 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 257 through 287
    Processing helix  chain 'K' and resid 295 through 298
    Processing helix  chain 'K' and resid 299 through 310
      removed outlier: 4.794A  pdb=" N   ASP K 307 " --> pdb=" O   ARG K 303 " (cutoff:3.500A)
      removed outlier: 5.288A  pdb=" N   SER K 308 " --> pdb=" O   LEU K 304 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 324 through 326
      No H-bonds generated for 'chain 'K' and resid 324 through 326'
    Processing helix  chain 'K' and resid 327 through 343
    Processing helix  chain 'A' and resid 10 through 29
    Processing helix  chain 'A' and resid 47 through 51
    Processing helix  chain 'A' and resid 72 through 81
      removed outlier: 3.608A  pdb=" N   VAL A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 90
      No H-bonds generated for 'chain 'A' and resid 88 through 90'
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 110 through 113
    Processing helix  chain 'A' and resid 114 through 128
      removed outlier: 3.557A  pdb=" N   GLN A 128 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 161
      removed outlier: 4.078A  pdb=" N   THR A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 197
      removed outlier: 3.524A  pdb=" N   ASN A 186 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   HIS A 192 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   THR A 193 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 218
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 4.408A  pdb=" N   SER A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 5.262A  pdb=" N   LEU A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 260
    Processing helix  chain 'A' and resid 277 through 284
      removed outlier: 3.997A  pdb=" N   TYR A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   HIS A 283 " --> pdb=" O   GLU A 279 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   GLU A 284 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 296
      removed outlier: 3.602A  pdb=" N   PHE A 296 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 301
    Processing helix  chain 'A' and resid 306 through 310
    Processing helix  chain 'A' and resid 324 through 337
      removed outlier: 3.591A  pdb=" N   VAL A 328 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 401
      removed outlier: 3.623A  pdb=" N   TRP A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LYS A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 411
      removed outlier: 4.080A  pdb=" N   TYR A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 436
      removed outlier: 3.910A  pdb=" N   PHE A 418 " --> pdb=" O   GLU A 414 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 10 through 28
    Processing helix  chain 'H' and resid 41 through 48
      removed outlier: 4.429A  pdb=" N   ARG H  48 " --> pdb=" O   LEU H  42 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 49 through 51
      No H-bonds generated for 'chain 'H' and resid 49 through 51'
    Processing helix  chain 'H' and resid 71 through 81
      removed outlier: 4.486A  pdb=" N   MET H  75 " --> pdb=" O   GLU H  71 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.745A  pdb=" N   PHE H  87 " --> pdb=" O   GLY H  84 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 88 through 90
      No H-bonds generated for 'chain 'H' and resid 88 through 90'
    Processing helix  chain 'H' and resid 102 through 108
    Processing helix  chain 'H' and resid 109 through 129
      removed outlier: 4.294A  pdb=" N   ASP H 116 " --> pdb=" O   ALA H 112 " (cutoff:3.500A)
      removed outlier: 5.283A  pdb=" N   SER H 117 " --> pdb=" O   GLU H 113 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   VAL H 118 " --> pdb=" O   LEU H 114 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 144 through 161
    Processing helix  chain 'H' and resid 182 through 198
      removed outlier: 3.545A  pdb=" N   GLN H 193 " --> pdb=" O   LEU H 189 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLU H 196 " --> pdb=" O   HIS H 192 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 206 through 216
    Processing helix  chain 'H' and resid 223 through 244
      removed outlier: 3.812A  pdb=" N   THR H 239 " --> pdb=" O   MET H 235 " (cutoff:3.500A)
      removed outlier: 5.001A  pdb=" N   CYS H 241 " --> pdb=" O   GLY H 237 " (cutoff:3.500A)
      removed outlier: 5.738A  pdb=" N   LEU H 242 " --> pdb=" O   VAL H 238 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 251 through 260
    Processing helix  chain 'H' and resid 278 through 282
      removed outlier: 3.603A  pdb=" N   GLN H 281 " --> pdb=" O   ARG H 278 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLN H 282 " --> pdb=" O   GLY H 279 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 278 through 282'
    Processing helix  chain 'H' and resid 287 through 297
      removed outlier: 3.549A  pdb=" N   ASP H 297 " --> pdb=" O   GLN H 293 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 298 through 301
    Processing helix  chain 'H' and resid 306 through 310
    Processing helix  chain 'H' and resid 324 through 339
    Processing helix  chain 'H' and resid 340 through 343
    Processing helix  chain 'H' and resid 384 through 401
      removed outlier: 4.205A  pdb=" N   ARG H 401 " --> pdb=" O   ALA H 397 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 404 through 411
      removed outlier: 4.123A  pdb=" N   TYR H 408 " --> pdb=" O   PHE H 404 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 414 through 436
      removed outlier: 4.071A  pdb=" N   PHE H 418 " --> pdb=" O   ASP H 414 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 63 through 65
      removed outlier: 9.068A  pdb=" N   TYR K  63 " --> pdb=" O   MET K   6 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   VAL K   8 " --> pdb=" O   TYR K  63 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   PHE K  65 " --> pdb=" O   VAL K   8 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   ILE K  10 " --> pdb=" O   PHE K  65 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   THR K  93 " --> pdb=" O   VAL K 316 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   ILE K 318 " --> pdb=" O   THR K  93 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   PHE K  95 " --> pdb=" O   ILE K 318 " (cutoff:3.500A)
      removed outlier: 7.385A  pdb=" N   ASN K 320 " --> pdb=" O   PHE K  95 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   TYR K  97 " --> pdb=" O   ASN K 320 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   SER K  92 " --> pdb=" O   CYS K 241 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   ILE K 243 " --> pdb=" O   SER K  92 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   VAL K  94 " --> pdb=" O   ILE K 243 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'K' and resid 63 through 65
      removed outlier: 9.068A  pdb=" N   TYR K  63 " --> pdb=" O   MET K   6 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   VAL K   8 " --> pdb=" O   TYR K  63 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   PHE K  65 " --> pdb=" O   VAL K   8 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   ILE K  10 " --> pdb=" O   PHE K  65 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   THR K  93 " --> pdb=" O   VAL K 316 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   ILE K 318 " --> pdb=" O   THR K  93 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   PHE K  95 " --> pdb=" O   ILE K 318 " (cutoff:3.500A)
      removed outlier: 7.385A  pdb=" N   ASN K 320 " --> pdb=" O   PHE K  95 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   TYR K  97 " --> pdb=" O   ASN K 320 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   SER K  92 " --> pdb=" O   CYS K 241 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   ILE K 243 " --> pdb=" O   SER K  92 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   VAL K  94 " --> pdb=" O   ILE K 243 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'K' and resid 28 through 32
      removed outlier: 6.536A  pdb=" N   MET K  35 " --> pdb=" O   LEU K  31 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'K' and resid 165 through 167
    Processing sheet with id=AA5, first strand: chain 'K' and resid 202 through 205
      removed outlier: 4.718A  pdb=" N   THR K 205 " --> pdb=" O   LYS K 209 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   LYS K 209 " --> pdb=" O   THR K 205 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 94
      removed outlier: 8.018A  pdb=" N   ILE A  93 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   PHE A  67 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 8.381A  pdb=" N   VAL A  66 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   GLU A   3 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   GLY A 134 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 4.880A  pdb=" N   SER A 140 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   SER A 165 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA8, first strand: chain 'A' and resid 269 through 273
      removed outlier: 6.816A  pdb=" N   ALA A 374 " --> pdb=" O   TYR A 319 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   TYR A 319 " --> pdb=" O   ALA A 374 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   CYS A 376 " --> pdb=" O   LEU A 317 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   LEU A 317 " --> pdb=" O   CYS A 376 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   LEU A 378 " --> pdb=" O   CYS A 315 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   CYS A 315 " --> pdb=" O   LEU A 378 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   ASN A 380 " --> pdb=" O   MET A 313 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 92 through 94
      removed outlier: 7.910A  pdb=" N   VAL H  93 " --> pdb=" O   ALA H  65 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   LEU H  67 " --> pdb=" O   VAL H  93 " (cutoff:3.500A)
      removed outlier: 8.471A  pdb=" N   ILE H  66 " --> pdb=" O   ILE H   4 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   HIS H   6 " --> pdb=" O   ILE H  66 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   VAL H  68 " --> pdb=" O   HIS H   6 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   GLN H   8 " --> pdb=" O   VAL H  68 " (cutoff:3.500A)
      removed outlier: 5.855A  pdb=" N   GLU H   3 " --> pdb=" O   LEU H 132 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLY H 134 " --> pdb=" O   GLU H   3 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   SER H 140 " --> pdb=" O   ALA H   9 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   GLN H 133 " --> pdb=" O   ILE H 165 " (cutoff:3.500A)
      removed outlier: 8.089A  pdb=" N   ASN H 167 " --> pdb=" O   GLN H 133 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   PHE H 135 " --> pdb=" O   ASN H 167 " (cutoff:3.500A)
      removed outlier: 7.710A  pdb=" N   PHE H 169 " --> pdb=" O   PHE H 135 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   LEU H 137 " --> pdb=" O   PHE H 169 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   VAL H 171 " --> pdb=" O   LEU H 137 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   HIS H 139 " --> pdb=" O   VAL H 171 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   MET H 166 " --> pdb=" O   GLU H 200 " (cutoff:3.500A)
      removed outlier: 8.012A  pdb=" N   TYR H 202 " --> pdb=" O   MET H 166 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   THR H 168 " --> pdb=" O   TYR H 202 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   ILE H 204 " --> pdb=" O   THR H 168 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   SER H 170 " --> pdb=" O   ILE H 204 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   THR H 201 " --> pdb=" O   PHE H 268 " (cutoff:3.500A)
      removed outlier: 7.419A  pdb=" N   CYS H 203 " --> pdb=" O   PRO H 270 " (cutoff:3.500A)
      removed outlier: 10.380A  pdb=" N   PHE H 272 " --> pdb=" O   CYS H 203 " (cutoff:3.500A)
      removed outlier: 13.171A  pdb=" N   ASP H 205 " --> pdb=" O   PHE H 272 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   PHE H 267 " --> pdb=" O   SER H 381 " (cutoff:3.500A)
      removed outlier: 5.068A  pdb=" N   SER H 381 " --> pdb=" O   PHE H 267 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   SER H 374 " --> pdb=" O   PHE H 319 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   PHE H 319 " --> pdb=" O   SER H 374 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   THR H 376 " --> pdb=" O   ALA H 317 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   ALA H 317 " --> pdb=" O   THR H 376 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   ILE H 378 " --> pdb=" O   VAL H 315 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   VAL H 315 " --> pdb=" O   ILE H 378 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   ASN H 380 " --> pdb=" O   LEU H 313 " (cutoff:3.500A)
      removed outlier: 8.453A  pdb=" N   LYS H 352 " --> pdb=" O   LEU H 313 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   VAL H 315 " --> pdb=" O   LYS H 352 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   ALA H 354 " --> pdb=" O   VAL H 315 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   ALA H 317 " --> pdb=" O   ALA H 354 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   CYS H 356 " --> pdb=" O   ALA H 317 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   PHE H 319 " --> pdb=" O   CYS H 356 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU H 248 " --> pdb=" O   VAL H 355 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 53 through 56
      removed outlier: 3.892A  pdb=" N   LYS H  60 " --> pdb=" O   ALA H  56 " (cutoff:3.500A)

    510 hydrogen bonds defined for protein.
    1464 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: 4.00

  Time building geometry restraints manager: 3.57 seconds

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

  Histogram of bond lengths:
        0.96 -     1.13: 2548
        1.13 -     1.31: 1627
        1.31 -     1.48: 3878
        1.48 -     1.66: 4066
        1.66 -     1.83: 105
  Bond restraints: 12224
  Sorted by residual:
  bond pdb=" NE  ARG K 297 "
       pdb=" HE  ARG K 297 "
    ideal  model  delta    sigma   weight residual
    0.860  1.050 -0.190 2.00e-02 2.50e+03 9.02e+01
  bond pdb=" NH1 ARG K 213 "
       pdb="HH11 ARG K 213 "
    ideal  model  delta    sigma   weight residual
    0.860  1.044 -0.184 2.00e-02 2.50e+03 8.47e+01
  bond pdb=" NE2 HIS K 194 "
       pdb=" HE2 HIS K 194 "
    ideal  model  delta    sigma   weight residual
    0.860  1.037 -0.177 2.00e-02 2.50e+03 7.80e+01
  bond pdb=" NE  ARG K  53 "
       pdb=" HE  ARG K  53 "
    ideal  model  delta    sigma   weight residual
    0.860  1.037 -0.177 2.00e-02 2.50e+03 7.80e+01
  bond pdb=" NE  ARG K 250 "
       pdb=" HE  ARG K 250 "
    ideal  model  delta    sigma   weight residual
    0.860  1.037 -0.177 2.00e-02 2.50e+03 7.80e+01
  ... (remaining 12219 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.07: 17412
        3.07 -     6.14: 1272
        6.14 -     9.21: 214
        9.21 -    12.28: 16
       12.28 -    15.35: 7
  Bond angle restraints: 18921
  Sorted by residual:
  angle pdb=" C   LYS K 139 "
        pdb=" N   VAL K 140 "
        pdb=" CA  VAL K 140 "
      ideal   model   delta    sigma   weight residual
     122.48  113.89    8.59 1.25e+00 6.40e-01 4.73e+01
  angle pdb=" C   SER K 322 "
        pdb=" N   PRO K 323 "
        pdb=" CA  PRO K 323 "
      ideal   model   delta    sigma   weight residual
     119.87  126.75   -6.88 1.04e+00 9.25e-01 4.38e+01
  angle pdb=" N   PRO K 169 "
        pdb=" CA  PRO K 169 "
        pdb=" C   PRO K 169 "
      ideal   model   delta    sigma   weight residual
     111.03  100.88   10.15 1.54e+00 4.22e-01 4.35e+01
  angle pdb=" C   ASN K 157 "
        pdb=" N   PRO K 158 "
        pdb=" CA  PRO K 158 "
      ideal   model   delta    sigma   weight residual
     119.82  126.15   -6.33 9.80e-01 1.04e+00 4.18e+01
  angle pdb=" N   ILE K 152 "
        pdb=" CA  ILE K 152 "
        pdb=" C   ILE K 152 "
      ideal   model   delta    sigma   weight residual
     107.80  117.06   -9.26 1.45e+00 4.76e-01 4.08e+01
  ... (remaining 18916 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.61: 6482
       33.61 -    67.21: 151
       67.21 -   100.82: 17
      100.82 -   134.42: 0
      134.42 -   168.03: 3
  Dihedral angle restraints: 6653
    sinusoidal: 3066
      harmonic: 3587
  Sorted by residual:
  dihedral pdb=" CD2 HIS K 332 "
           pdb=" CG  HIS K 332 "
           pdb=" ND1 HIS K 332 "
           pdb=" HD1 HIS K 332 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -136.43  -43.57     0      5.00e+00 4.00e-02 7.59e+01
  dihedral pdb=" C5' GTP A 501 "
           pdb=" O5' GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" O3A GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -122.70 -168.03     1      2.00e+01 2.50e-03 4.75e+01
  dihedral pdb=" C8  GTP A 501 "
           pdb=" C1' GTP A 501 "
           pdb=" N9  GTP A 501 "
           pdb=" O4' GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -51.73  156.33     1      2.00e+01 2.50e-03 4.60e+01
  ... (remaining 6650 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 997
       0.079 -    0.158: 337
       0.158 -    0.237: 96
       0.237 -    0.316: 21
       0.316 -    0.395: 3
  Chirality restraints: 1454
  Sorted by residual:
  chirality pdb=" CA  HIS A 197 "
            pdb=" N   HIS A 197 "
            pdb=" C   HIS A 197 "
            pdb=" CB  HIS A 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.40 2.00e-01 2.50e+01 3.91e+00
  chirality pdb=" CA  THR H 109 "
            pdb=" N   THR H 109 "
            pdb=" C   THR H 109 "
            pdb=" CB  THR H 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.20    0.33 2.00e-01 2.50e+01 2.73e+00
  chirality pdb=" C3' G2P H 501 "
            pdb=" C2' G2P H 501 "
            pdb=" C4' G2P H 501 "
            pdb=" O3' G2P H 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.38   -0.33 2.00e-01 2.50e+01 2.71e+00
  ... (remaining 1451 not shown)

  Planarity restraints: 2042
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS K 332 "    0.154 2.00e-02 2.50e+03   1.62e-01 5.92e+02
        pdb=" CG  HIS K 332 "    0.077 2.00e-02 2.50e+03
        pdb=" ND1 HIS K 332 "    0.148 2.00e-02 2.50e+03
        pdb=" CD2 HIS K 332 "   -0.042 2.00e-02 2.50e+03
        pdb=" CE1 HIS K 332 "    0.082 2.00e-02 2.50e+03
        pdb=" NE2 HIS K 332 "   -0.037 2.00e-02 2.50e+03
        pdb=" HD1 HIS K 332 "   -0.382 2.00e-02 2.50e+03
        pdb=" HD2 HIS K 332 "   -0.123 2.00e-02 2.50e+03
        pdb=" HE1 HIS K 332 "    0.122 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR K   4 "   -0.072 2.00e-02 2.50e+03   2.82e-02 2.38e+01
        pdb=" CG  TYR K   4 "    0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR K   4 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TYR K   4 "    0.024 2.00e-02 2.50e+03
        pdb=" CE1 TYR K   4 "    0.011 2.00e-02 2.50e+03
        pdb=" CE2 TYR K   4 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  TYR K   4 "   -0.007 2.00e-02 2.50e+03
        pdb=" OH  TYR K   4 "   -0.047 2.00e-02 2.50e+03
        pdb=" HD1 TYR K   4 "    0.016 2.00e-02 2.50e+03
        pdb=" HD2 TYR K   4 "    0.015 2.00e-02 2.50e+03
        pdb=" HE1 TYR K   4 "    0.005 2.00e-02 2.50e+03
        pdb=" HE2 TYR K   4 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR K  75 "    0.070 2.00e-02 2.50e+03   2.79e-02 2.33e+01
        pdb=" CG  TYR K  75 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD1 TYR K  75 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD2 TYR K  75 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR K  75 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR K  75 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  TYR K  75 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR K  75 "    0.037 2.00e-02 2.50e+03
        pdb=" HD1 TYR K  75 "   -0.034 2.00e-02 2.50e+03
        pdb=" HD2 TYR K  75 "   -0.010 2.00e-02 2.50e+03
        pdb=" HE1 TYR K  75 "    0.015 2.00e-02 2.50e+03
        pdb=" HE2 TYR K  75 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 2039 not shown)

  Histogram of nonbonded interaction distances:
        0.85 -     1.60: 21
        1.60 -     2.35: 1340
        2.35 -     3.10: 21805
        3.10 -     3.85: 37266
        3.85 -     4.60: 58508
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 118940
  Sorted by model distance:
  nonbonded pdb="HG11 VAL K  48 "
            pdb=" OD1 ASP A 431 "
     model   vdw
     0.853 2.620
  nonbonded pdb="HD21 ASN K  52 "
            pdb=" CE  LYS A 430 "
     model   vdw
     0.973 2.750
  nonbonded pdb=" OE1 GLU K  32 "
            pdb=" HZ3 LYS K  34 "
     model   vdw
     1.023 2.450
  nonbonded pdb=" HZ1 LYS K 336 "
            pdb=" OG  SER A 419 "
     model   vdw
     1.089 1.960
  nonbonded pdb="HH12 ARG K 297 "
            pdb=" CB  GLU H 431 "
     model   vdw
     1.109 2.200
  ... (remaining 118935 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.060
  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:             0.270
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     27.850
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6294
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.256   9674  Z= 0.767
  Angle     :  1.591  14.075  13107  Z= 1.078
  Chirality :  0.088   0.395   1454
  Planarity :  0.008   0.074   1705
  Dihedral  : 14.711 168.027   3606
  Min Nonbonded Distance : 1.386

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.02 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  5.02 %
    Favored  : 94.49 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.23), residues: 1193
  helix:  0.63 (0.20), residues: 518
  sheet: -0.25 (0.36), residues: 209
  loop : -0.52 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP A  21 
 HIS   0.015   0.002   HIS A  88 
 PHE   0.033   0.004   PHE K 179 
 TYR   0.063   0.006   TYR K   4 
 ARG   0.006   0.001   ARG A 243 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18762 (  481)
  hydrogen bonds       : angle       7.57135 ( 1464)
  covalent geometry    : bond        0.01179 ( 9670)
  covalent geometry    : angle       1.59052 (13107)
  Misc. bond           : bond        0.14270 (    4)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   17 is missing expected H atoms. Skipping.
Residue LEU   31 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue SER   45 is missing expected H atoms. Skipping.
Residue SER   54 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue VAL   60 is missing expected H atoms. Skipping.
Residue SER   70 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  131 is missing expected H atoms. Skipping.
Residue ILE  134 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue VAL  165 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue VAL  173 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue VAL  231 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue VAL  316 is missing expected H atoms. Skipping.
Evaluate side-chains
  354 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 349
  time to evaluate  : 1.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  150 GLU cc_start: 0.5124 (mm-30) cc_final: 0.4371 (mm-30)
REVERT: K  215 HIS cc_start: 0.5474 (m-70) cc_final: 0.5006 (m90)
REVERT: K  332 HIS cc_start: 0.6504 (t70) cc_final: 0.5207 (t70)
REVERT: A   16 ILE cc_start: 0.7561 (mt) cc_final: 0.7023 (mt)
REVERT: A  317 LEU cc_start: 0.8297 (mm) cc_final: 0.8052 (mp)
REVERT: A  346 TRP cc_start: 0.5289 (p-90) cc_final: 0.2739 (t60)
REVERT: H   19 LYS cc_start: 0.7754 (tptt) cc_final: 0.7503 (tppt)
REVERT: H  384 ILE cc_start: 0.8279 (mm) cc_final: 0.7750 (mt)
  outliers start: 5
  outliers final: 1
  residues processed: 354
  average time/residue: 0.3500
  time to fit residues: 162.1154
Evaluate side-chains
  207 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 206
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:   10.0000
   chunk 89 optimal weight:   20.0000
   chunk 49 optimal weight:    0.0870
   chunk 30 optimal weight:    6.9990
   chunk 60 optimal weight:    9.9990
   chunk 47 optimal weight:    5.9990
   chunk 92 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 68 optimal weight:    5.9990
   chunk 107 optimal weight:   30.0000
   overall best weight:    4.8166

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

Flipped N/Q/H residues before XYZ refinement:
K 133 GLN
** K 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 197 HIS
A 226 ASN
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 406 HIS
** H   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 136 GLN
H 139 HIS
** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 406 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.091494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.068315 restraints weight = 56149.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.071346 restraints weight = 28674.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.073307 restraints weight = 18490.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.4030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   9674  Z= 0.182
  Angle     :  0.641  12.577  13107  Z= 0.354
  Chirality :  0.043   0.197   1454
  Planarity :  0.009   0.315   1705
  Dihedral  : 11.106 173.569   1351
  Min Nonbonded Distance : 1.779

Molprobity Statistics.
  All-atom Clashscore : 28.92
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.51 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.51 %
    Favored  : 97.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.24), residues: 1193
  helix:  1.41 (0.22), residues: 532
  sheet:  0.06 (0.34), residues: 225
  loop : -0.55 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 407 
 HIS   0.007   0.001   HIS K 332 
 PHE   0.018   0.002   PHE H 262 
 TYR   0.026   0.002   TYR H 432 
 ARG   0.017   0.001   ARG K 297 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05656 (  481)
  hydrogen bonds       : angle       5.55111 ( 1464)
  covalent geometry    : bond        0.00370 ( 9670)
  covalent geometry    : angle       0.64079 (13107)
  Misc. bond           : bond        0.00551 (    4)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   17 is missing expected H atoms. Skipping.
Residue LEU   31 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue SER   45 is missing expected H atoms. Skipping.
Residue SER   54 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue VAL   60 is missing expected H atoms. Skipping.
Residue SER   70 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  131 is missing expected H atoms. Skipping.
Residue ILE  134 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue VAL  165 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue VAL  173 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue VAL  231 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue VAL  316 is missing expected H atoms. Skipping.
Evaluate side-chains
  244 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 242
  time to evaluate  : 1.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  150 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7263 (mm-30)
REVERT: K  190 MET cc_start: 0.9487 (ttp) cc_final: 0.9077 (tmm)
REVERT: K  255 ASN cc_start: 0.6541 (m110) cc_final: 0.6145 (m110)
REVERT: K  266 ASN cc_start: 0.9402 (m-40) cc_final: 0.9140 (m110)
REVERT: A   35 GLN cc_start: 0.7742 (tm-30) cc_final: 0.7432 (tm-30)
REVERT: A   70 LEU cc_start: 0.8336 (mt) cc_final: 0.8117 (mt)
REVERT: A  101 ASN cc_start: 0.9127 (m-40) cc_final: 0.8900 (m110)
REVERT: A  313 MET cc_start: 0.8337 (mtp) cc_final: 0.8120 (mtt)
REVERT: A  368 LEU cc_start: 0.8055 (mm) cc_final: 0.7853 (mm)
REVERT: H  102 ASN cc_start: 0.8067 (t0) cc_final: 0.7168 (t0)
REVERT: H  105 LYS cc_start: 0.8612 (mtpt) cc_final: 0.8334 (mtpt)
REVERT: H  110 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8392 (tp30)
REVERT: H  116 ASP cc_start: 0.9260 (m-30) cc_final: 0.9020 (m-30)
REVERT: H  267 PHE cc_start: 0.9009 (m-80) cc_final: 0.8714 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 242
  average time/residue: 0.3021
  time to fit residues: 100.2060
Evaluate side-chains
  183 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 16 optimal weight:   30.0000
   chunk 80 optimal weight:   20.0000
   chunk 34 optimal weight:   30.0000
   chunk 28 optimal weight:   20.0000
   chunk 14 optimal weight:   20.0000
   chunk 96 optimal weight:   20.0000
   chunk 24 optimal weight:   40.0000
   chunk 30 optimal weight:    2.9990
   chunk 94 optimal weight:   30.0000
   chunk 46 optimal weight:    9.9990
   chunk 81 optimal weight:    8.9990
   overall best weight:   12.3994

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

Flipped N/Q/H residues before XYZ refinement:
K 202 GLN
** K 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  31 GLN
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 300 ASN
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  28 HIS
** H  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 101 ASN
** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.085831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.063271 restraints weight = 59189.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.066040 restraints weight = 30742.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.067853 restraints weight = 19989.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.5301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.152   9674  Z= 0.313
  Angle     :  0.758  12.756  13107  Z= 0.414
  Chirality :  0.044   0.175   1454
  Planarity :  0.009   0.285   1705
  Dihedral  : 10.903 174.799   1351
  Min Nonbonded Distance : 1.745

Molprobity Statistics.
  All-atom Clashscore : 44.66
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.11 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.86 %
    Favored  : 96.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.24), residues: 1193
  helix:  0.61 (0.21), residues: 534
  sheet: -0.23 (0.34), residues: 231
  loop : -0.82 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 346 
 HIS   0.013   0.002   HIS A   8 
 PHE   0.024   0.003   PHE H  87 
 TYR   0.024   0.002   TYR H  53 
 ARG   0.031   0.001   ARG K 297 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05499 (  481)
  hydrogen bonds       : angle       5.74224 ( 1464)
  covalent geometry    : bond        0.00633 ( 9670)
  covalent geometry    : angle       0.75815 (13107)
  Misc. bond           : bond        0.00473 (    4)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   17 is missing expected H atoms. Skipping.
Residue LEU   31 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue SER   45 is missing expected H atoms. Skipping.
Residue SER   54 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue VAL   60 is missing expected H atoms. Skipping.
Residue SER   70 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  131 is missing expected H atoms. Skipping.
Residue ILE  134 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue VAL  165 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue VAL  173 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue VAL  231 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue VAL  316 is missing expected H atoms. Skipping.
Evaluate side-chains
  195 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 194
  time to evaluate  : 1.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  150 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7133 (mm-30)
REVERT: K  255 ASN cc_start: 0.6628 (m110) cc_final: 0.6251 (m110)
REVERT: K  259 MET cc_start: 0.8988 (mmm) cc_final: 0.8463 (tpp)
REVERT: K  266 ASN cc_start: 0.9475 (m-40) cc_final: 0.9234 (t0)
REVERT: K  278 ILE cc_start: 0.9590 (mt) cc_final: 0.9357 (tt)
REVERT: K  336 LYS cc_start: 0.9103 (mmtt) cc_final: 0.8845 (mtmt)
REVERT: A   35 GLN cc_start: 0.8077 (tm-30) cc_final: 0.7805 (tm-30)
REVERT: A  101 ASN cc_start: 0.9260 (m-40) cc_final: 0.8952 (m-40)
REVERT: A  103 TYR cc_start: 0.8633 (t80) cc_final: 0.8316 (t80)
REVERT: A  313 MET cc_start: 0.8546 (mtp) cc_final: 0.8284 (mtp)
REVERT: A  413 MET cc_start: 0.8288 (mmm) cc_final: 0.7969 (mmp)
REVERT: H  102 ASN cc_start: 0.8176 (t0) cc_final: 0.7510 (t0)
REVERT: H  105 LYS cc_start: 0.8733 (mtpt) cc_final: 0.8372 (mtpt)
REVERT: H  110 GLU cc_start: 0.8921 (mm-30) cc_final: 0.7780 (tt0)
REVERT: H  113 GLU cc_start: 0.8301 (pp20) cc_final: 0.8043 (pp20)
REVERT: H  416 MET cc_start: 0.9023 (tpp) cc_final: 0.8801 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 194
  average time/residue: 0.3165
  time to fit residues: 83.8571
Evaluate side-chains
  148 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 67 optimal weight:    8.9990
   chunk 5 optimal weight:   30.0000
   chunk 91 optimal weight:    5.9990
   chunk 37 optimal weight:   20.0000
   chunk 63 optimal weight:    0.0470
   chunk 48 optimal weight:   10.0000
   chunk 68 optimal weight:   10.0000
   chunk 33 optimal weight:    5.9990
   chunk 94 optimal weight:   10.0000
   chunk 93 optimal weight:   30.0000
   overall best weight:    4.4086

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

Flipped N/Q/H residues before XYZ refinement:
K   5 ASN
** K 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  59 ASN
H 101 ASN
** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.087665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.064840 restraints weight = 56311.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.067684 restraints weight = 29172.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.069513 restraints weight = 18933.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.5643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9674  Z= 0.147
  Angle     :  0.578  15.382  13107  Z= 0.311
  Chirality :  0.042   0.178   1454
  Planarity :  0.006   0.170   1705
  Dihedral  :  9.668 171.564   1351
  Min Nonbonded Distance : 1.797

Molprobity Statistics.
  All-atom Clashscore : 38.05
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.44 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  1.35 %
    Favored  : 98.36 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.24), residues: 1193
  helix:  1.20 (0.22), residues: 533
  sheet: -0.43 (0.34), residues: 233
  loop : -0.78 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 346 
 HIS   0.007   0.001   HIS A  88 
 PHE   0.015   0.002   PHE K 293 
 TYR   0.026   0.002   TYR H 432 
 ARG   0.020   0.001   ARG K 297 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04609 (  481)
  hydrogen bonds       : angle       5.23297 ( 1464)
  covalent geometry    : bond        0.00290 ( 9670)
  covalent geometry    : angle       0.57796 (13107)
  Misc. bond           : bond        0.00440 (    4)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   17 is missing expected H atoms. Skipping.
Residue LEU   31 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue SER   45 is missing expected H atoms. Skipping.
Residue SER   54 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue VAL   60 is missing expected H atoms. Skipping.
Residue SER   70 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  131 is missing expected H atoms. Skipping.
Residue ILE  134 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue VAL  165 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue VAL  173 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue VAL  231 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue VAL  316 is missing expected H atoms. Skipping.
Evaluate side-chains
  196 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 193
  time to evaluate  : 1.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  150 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7729 (mm-30)
REVERT: K  190 MET cc_start: 0.9548 (ttp) cc_final: 0.9104 (tmm)
REVERT: K  259 MET cc_start: 0.9078 (mmm) cc_final: 0.8364 (tpp)
REVERT: K  278 ILE cc_start: 0.9560 (mt) cc_final: 0.9309 (tt)
REVERT: K  336 LYS cc_start: 0.9028 (mmtt) cc_final: 0.8693 (mtmt)
REVERT: A   35 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7709 (tm-30)
REVERT: A  101 ASN cc_start: 0.9245 (m-40) cc_final: 0.8976 (m-40)
REVERT: A  194 THR cc_start: 0.9012 (m) cc_final: 0.8658 (t)
REVERT: A  313 MET cc_start: 0.8380 (mtp) cc_final: 0.8085 (mtt)
REVERT: A  413 MET cc_start: 0.8141 (mmm) cc_final: 0.7840 (mmp)
REVERT: H  101 ASN cc_start: 0.8478 (m-40) cc_final: 0.8158 (m-40)
REVERT: H  102 ASN cc_start: 0.8166 (t0) cc_final: 0.7940 (t0)
REVERT: H  416 MET cc_start: 0.8813 (tpp) cc_final: 0.8515 (tpp)
  outliers start: 3
  outliers final: 2
  residues processed: 195
  average time/residue: 0.3002
  time to fit residues: 79.6834
Evaluate side-chains
  158 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 156
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 110 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 13 optimal weight:   20.0000
   chunk 27 optimal weight:   20.0000
   chunk 88 optimal weight:    9.9990
   chunk 74 optimal weight:    7.9990
   chunk 89 optimal weight:    5.9990
   chunk 108 optimal weight:   20.0000
   chunk 95 optimal weight:    0.9990
   chunk 17 optimal weight:   20.0000
   chunk 85 optimal weight:   10.0000
   overall best weight:    4.3588

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

Flipped N/Q/H residues before XYZ refinement:
** K 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 300 ASN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  15 GLN
** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.087054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.064221 restraints weight = 56074.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.067083 restraints weight = 28901.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.068958 restraints weight = 18698.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.6043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9674  Z= 0.145
  Angle     :  0.532  12.189  13107  Z= 0.288
  Chirality :  0.041   0.174   1454
  Planarity :  0.003   0.031   1705
  Dihedral  :  9.309 168.907   1351
  Min Nonbonded Distance : 1.813

Molprobity Statistics.
  All-atom Clashscore : 39.65
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.02 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.25), residues: 1193
  helix:  1.31 (0.22), residues: 534
  sheet: -0.32 (0.35), residues: 225
  loop : -0.78 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  21 
 HIS   0.005   0.001   HIS A   8 
 PHE   0.013   0.001   PHE K 293 
 TYR   0.016   0.001   TYR K  75 
 ARG   0.012   0.000   ARG K  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04302 (  481)
  hydrogen bonds       : angle       5.10784 ( 1464)
  covalent geometry    : bond        0.00292 ( 9670)
  covalent geometry    : angle       0.53159 (13107)
  Misc. bond           : bond        0.00607 (    4)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   17 is missing expected H atoms. Skipping.
Residue LEU   31 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue SER   45 is missing expected H atoms. Skipping.
Residue SER   54 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue VAL   60 is missing expected H atoms. Skipping.
Residue SER   70 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  131 is missing expected H atoms. Skipping.
Residue ILE  134 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue VAL  165 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue VAL  173 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue VAL  231 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue VAL  316 is missing expected H atoms. Skipping.
Evaluate side-chains
  187 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 1.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  150 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7656 (mm-30)
REVERT: K  190 MET cc_start: 0.9560 (ttp) cc_final: 0.9132 (tmm)
REVERT: K  255 ASN cc_start: 0.7083 (m110) cc_final: 0.6668 (m110)
REVERT: K  259 MET cc_start: 0.8943 (mmm) cc_final: 0.8356 (tpp)
REVERT: K  278 ILE cc_start: 0.9568 (mt) cc_final: 0.9327 (tt)
REVERT: A   35 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7718 (tm-30)
REVERT: A  101 ASN cc_start: 0.9289 (m-40) cc_final: 0.8994 (m-40)
REVERT: A  194 THR cc_start: 0.9001 (m) cc_final: 0.8676 (t)
REVERT: A  313 MET cc_start: 0.8367 (mtp) cc_final: 0.8012 (mtt)
REVERT: A  413 MET cc_start: 0.8158 (mmm) cc_final: 0.7777 (mmp)
REVERT: H   68 VAL cc_start: 0.8514 (t) cc_final: 0.7947 (m)
REVERT: H  416 MET cc_start: 0.8880 (tpp) cc_final: 0.8566 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.2931
  time to fit residues: 75.8392
Evaluate side-chains
  151 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 91 optimal weight:    9.9990
   chunk 110 optimal weight:    9.9990
   chunk 21 optimal weight:   30.0000
   chunk 72 optimal weight:   10.0000
   chunk 79 optimal weight:    4.9990
   chunk 108 optimal weight:   20.0000
   chunk 44 optimal weight:   20.0000
   chunk 34 optimal weight:   30.0000
   chunk 71 optimal weight:   20.0000
   chunk 70 optimal weight:   10.0000
   chunk 28 optimal weight:   20.0000
   overall best weight:    8.9994

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

Flipped N/Q/H residues before XYZ refinement:
** K 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 380 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 = 0.3613 r_free = 0.3613 target = 0.085256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.062424 restraints weight = 58428.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.065189 restraints weight = 30323.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.066965 restraints weight = 19710.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.6495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.089   9674  Z= 0.230
  Angle     :  0.612  15.968  13107  Z= 0.330
  Chirality :  0.042   0.177   1454
  Planarity :  0.007   0.253   1705
  Dihedral  :  9.393 168.263   1351
  Min Nonbonded Distance : 1.764

Molprobity Statistics.
  All-atom Clashscore : 46.32
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.03 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.71 %
    Favored  : 97.20 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.24), residues: 1193
  helix:  1.12 (0.22), residues: 534
  sheet: -0.39 (0.36), residues: 217
  loop : -0.97 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 346 
 HIS   0.008   0.001   HIS A   8 
 PHE   0.029   0.002   PHE K 126 
 TYR   0.017   0.002   TYR H 312 
 ARG   0.037   0.001   ARG K 297 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04367 (  481)
  hydrogen bonds       : angle       5.25723 ( 1464)
  covalent geometry    : bond        0.00471 ( 9670)
  covalent geometry    : angle       0.61183 (13107)
  Misc. bond           : bond        0.01072 (    4)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   17 is missing expected H atoms. Skipping.
Residue LEU   31 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue SER   45 is missing expected H atoms. Skipping.
Residue SER   54 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue VAL   60 is missing expected H atoms. Skipping.
Residue SER   70 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  131 is missing expected H atoms. Skipping.
Residue ILE  134 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue VAL  165 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue VAL  173 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue VAL  231 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue VAL  316 is missing expected H atoms. Skipping.
Evaluate side-chains
  176 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 1.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  150 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7387 (mm-30)
REVERT: K  190 MET cc_start: 0.9588 (ttp) cc_final: 0.9112 (tmm)
REVERT: K  255 ASN cc_start: 0.7171 (m110) cc_final: 0.6811 (m110)
REVERT: K  259 MET cc_start: 0.8942 (mmm) cc_final: 0.8395 (tpp)
REVERT: K  266 ASN cc_start: 0.9450 (m-40) cc_final: 0.9229 (t0)
REVERT: K  278 ILE cc_start: 0.9580 (mt) cc_final: 0.9356 (tt)
REVERT: K  300 LYS cc_start: 0.9060 (mmmm) cc_final: 0.8853 (mmtp)
REVERT: A   35 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7978 (tm-30)
REVERT: A  101 ASN cc_start: 0.9341 (m-40) cc_final: 0.9006 (m-40)
REVERT: A  154 MET cc_start: 0.9086 (tpt) cc_final: 0.8786 (tpp)
REVERT: A  413 MET cc_start: 0.8475 (mmm) cc_final: 0.7914 (mmp)
REVERT: A  431 ASP cc_start: 0.8629 (m-30) cc_final: 0.8390 (m-30)
REVERT: H   68 VAL cc_start: 0.8539 (t) cc_final: 0.8266 (t)
REVERT: H  105 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8638 (mtpt)
REVERT: H  127 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8866 (mt-10)
REVERT: H  398 MET cc_start: 0.7978 (mmp) cc_final: 0.7010 (mtt)
REVERT: H  416 MET cc_start: 0.8907 (tpp) cc_final: 0.8627 (tpp)
  outliers start: 1
  outliers final: 1
  residues processed: 175
  average time/residue: 0.3621
  time to fit residues: 91.7046
Evaluate side-chains
  144 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 143
  time to evaluate  : 1.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 77 optimal weight:    7.9990
   chunk 33 optimal weight:   20.0000
   chunk 91 optimal weight:    8.9990
   chunk 59 optimal weight:    9.9990
   chunk 41 optimal weight:   20.0000
   chunk 25 optimal weight:   10.0000
   chunk 80 optimal weight:   20.0000
   chunk 3 optimal weight:   20.0000
   chunk 54 optimal weight:    7.9990
   chunk 51 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    7.5990

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

Flipped N/Q/H residues before XYZ refinement:
K 343 ASN
** A  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 249 ASN
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.085107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.062348 restraints weight = 58327.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.065055 restraints weight = 30636.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.066862 restraints weight = 20143.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.6818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   9674  Z= 0.196
  Angle     :  0.564  10.955  13107  Z= 0.305
  Chirality :  0.041   0.187   1454
  Planarity :  0.004   0.065   1705
  Dihedral  :  9.209 166.651   1351
  Min Nonbonded Distance : 1.759

Molprobity Statistics.
  All-atom Clashscore : 46.37
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.78 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.25), residues: 1193
  helix:  1.06 (0.22), residues: 534
  sheet: -0.66 (0.36), residues: 222
  loop : -0.96 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 346 
 HIS   0.006   0.001   HIS A   8 
 PHE   0.015   0.002   PHE H 395 
 TYR   0.015   0.002   TYR A 432 
 ARG   0.006   0.001   ARG K 340 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04175 (  481)
  hydrogen bonds       : angle       5.17716 ( 1464)
  covalent geometry    : bond        0.00401 ( 9670)
  covalent geometry    : angle       0.56356 (13107)
  Misc. bond           : bond        0.00415 (    4)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   17 is missing expected H atoms. Skipping.
Residue LEU   31 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue SER   45 is missing expected H atoms. Skipping.
Residue SER   54 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue VAL   60 is missing expected H atoms. Skipping.
Residue SER   70 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  131 is missing expected H atoms. Skipping.
Residue ILE  134 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue VAL  165 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue VAL  173 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue VAL  231 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue VAL  316 is missing expected H atoms. Skipping.
Evaluate side-chains
  174 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 2.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  150 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7438 (mm-30)
REVERT: K  190 MET cc_start: 0.9629 (ttp) cc_final: 0.9120 (tmm)
REVERT: K  255 ASN cc_start: 0.7050 (m110) cc_final: 0.6712 (m110)
REVERT: K  259 MET cc_start: 0.8961 (mmm) cc_final: 0.8313 (tpp)
REVERT: K  266 ASN cc_start: 0.9417 (m-40) cc_final: 0.9210 (t0)
REVERT: K  278 ILE cc_start: 0.9582 (mt) cc_final: 0.9340 (tp)
REVERT: K  300 LYS cc_start: 0.9073 (mmmm) cc_final: 0.8857 (mmtp)
REVERT: A   35 GLN cc_start: 0.8340 (tm-30) cc_final: 0.8034 (tm-30)
REVERT: A  101 ASN cc_start: 0.9323 (m-40) cc_final: 0.8958 (m-40)
REVERT: A  154 MET cc_start: 0.9078 (tpt) cc_final: 0.8792 (tpp)
REVERT: A  251 ASP cc_start: 0.8733 (t0) cc_final: 0.8169 (m-30)
REVERT: A  413 MET cc_start: 0.8537 (mmm) cc_final: 0.7882 (mmp)
REVERT: A  431 ASP cc_start: 0.8522 (m-30) cc_final: 0.8300 (m-30)
REVERT: H  105 LYS cc_start: 0.8900 (mtpt) cc_final: 0.8640 (mtpt)
REVERT: H  127 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8885 (mt-10)
REVERT: H  218 LYS cc_start: 0.9483 (mtmm) cc_final: 0.9269 (ptpp)
REVERT: H  384 ILE cc_start: 0.8708 (mm) cc_final: 0.8424 (mm)
REVERT: H  398 MET cc_start: 0.7821 (mmp) cc_final: 0.6966 (mtt)
REVERT: H  416 MET cc_start: 0.8821 (tpp) cc_final: 0.8549 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.3608
  time to fit residues: 87.1851
Evaluate side-chains
  146 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 1.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 34 optimal weight:   20.0000
   chunk 107 optimal weight:   20.0000
   chunk 47 optimal weight:   20.0000
   chunk 68 optimal weight:   20.0000
   chunk 29 optimal weight:    8.9990
   chunk 94 optimal weight:   10.0000
   chunk 27 optimal weight:   20.0000
   chunk 96 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 105 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 349 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 = 0.3610 r_free = 0.3610 target = 0.085024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.061700 restraints weight = 57877.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.064504 restraints weight = 29750.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.066359 restraints weight = 19376.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.7002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9674  Z= 0.171
  Angle     :  0.545   8.922  13107  Z= 0.294
  Chirality :  0.041   0.184   1454
  Planarity :  0.004   0.057   1705
  Dihedral  :  9.152 166.030   1351
  Min Nonbonded Distance : 1.775

Molprobity Statistics.
  All-atom Clashscore : 45.20
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.78 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.25), residues: 1193
  helix:  1.15 (0.22), residues: 535
  sheet: -0.80 (0.36), residues: 222
  loop : -0.98 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 346 
 HIS   0.005   0.001   HIS A   8 
 PHE   0.021   0.002   PHE H 418 
 TYR   0.013   0.001   TYR H 432 
 ARG   0.012   0.001   ARG K 297 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04043 (  481)
  hydrogen bonds       : angle       5.06107 ( 1464)
  covalent geometry    : bond        0.00346 ( 9670)
  covalent geometry    : angle       0.54484 (13107)
  Misc. bond           : bond        0.00344 (    4)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   17 is missing expected H atoms. Skipping.
Residue LEU   31 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue SER   45 is missing expected H atoms. Skipping.
Residue SER   54 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue VAL   60 is missing expected H atoms. Skipping.
Residue SER   70 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  131 is missing expected H atoms. Skipping.
Residue ILE  134 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue VAL  165 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue VAL  173 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue VAL  231 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue VAL  316 is missing expected H atoms. Skipping.
Evaluate side-chains
  175 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 1.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  150 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7421 (mm-30)
REVERT: K  190 MET cc_start: 0.9638 (ttp) cc_final: 0.9136 (tmm)
REVERT: K  215 HIS cc_start: 0.8590 (m-70) cc_final: 0.8276 (m90)
REVERT: K  255 ASN cc_start: 0.7042 (m110) cc_final: 0.6703 (m110)
REVERT: K  259 MET cc_start: 0.8951 (mmm) cc_final: 0.8362 (tpp)
REVERT: K  266 ASN cc_start: 0.9404 (m-40) cc_final: 0.9189 (t0)
REVERT: K  278 ILE cc_start: 0.9573 (mt) cc_final: 0.9342 (tp)
REVERT: K  300 LYS cc_start: 0.9110 (mmmm) cc_final: 0.8887 (mmtp)
REVERT: A   35 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8068 (tm-30)
REVERT: A  101 ASN cc_start: 0.9312 (m-40) cc_final: 0.8952 (m-40)
REVERT: A  154 MET cc_start: 0.9075 (tpt) cc_final: 0.8800 (tpp)
REVERT: A  194 THR cc_start: 0.9182 (m) cc_final: 0.8887 (t)
REVERT: A  251 ASP cc_start: 0.8702 (t0) cc_final: 0.8153 (m-30)
REVERT: A  413 MET cc_start: 0.8497 (mmm) cc_final: 0.7847 (mmp)
REVERT: A  431 ASP cc_start: 0.8451 (m-30) cc_final: 0.8216 (m-30)
REVERT: H   75 MET cc_start: 0.8825 (mmm) cc_final: 0.8314 (mpp)
REVERT: H  105 LYS cc_start: 0.8894 (mtpt) cc_final: 0.8686 (mtpt)
REVERT: H  127 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8914 (mt-10)
REVERT: H  269 MET cc_start: 0.8102 (ptm) cc_final: 0.7881 (ptm)
REVERT: H  398 MET cc_start: 0.7845 (mmp) cc_final: 0.6985 (mtt)
REVERT: H  416 MET cc_start: 0.8746 (tpp) cc_final: 0.8479 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.4341
  time to fit residues: 105.7311
Evaluate side-chains
  147 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9990
   chunk 117 optimal weight:   20.0000
   chunk 90 optimal weight:   30.0000
   chunk 97 optimal weight:   20.0000
   chunk 28 optimal weight:   20.0000
   chunk 24 optimal weight:   10.0000
   chunk 80 optimal weight:   20.0000
   chunk 21 optimal weight:    6.9990
   chunk 52 optimal weight:    0.1980
   chunk 93 optimal weight:   20.0000
   overall best weight:    5.6390

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
** A  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 349 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 = 0.3604 r_free = 0.3604 target = 0.085091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.061629 restraints weight = 57103.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.064423 restraints weight = 29380.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.066289 restraints weight = 19082.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.7238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9674  Z= 0.154
  Angle     :  0.522   7.979  13107  Z= 0.280
  Chirality :  0.041   0.168   1454
  Planarity :  0.004   0.062   1705
  Dihedral  :  9.026 166.197   1351
  Min Nonbonded Distance : 1.792

Molprobity Statistics.
  All-atom Clashscore : 43.49
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.20 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.25), residues: 1193
  helix:  1.24 (0.22), residues: 535
  sheet: -0.69 (0.36), residues: 215
  loop : -1.03 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 103 
 HIS   0.004   0.001   HIS A  88 
 PHE   0.015   0.001   PHE H 418 
 TYR   0.024   0.001   TYR H 224 
 ARG   0.007   0.000   ARG K 340 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03842 (  481)
  hydrogen bonds       : angle       4.95788 ( 1464)
  covalent geometry    : bond        0.00312 ( 9670)
  covalent geometry    : angle       0.52243 (13107)
  Misc. bond           : bond        0.00462 (    4)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   17 is missing expected H atoms. Skipping.
Residue LEU   31 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue SER   45 is missing expected H atoms. Skipping.
Residue SER   54 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue VAL   60 is missing expected H atoms. Skipping.
Residue SER   70 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  131 is missing expected H atoms. Skipping.
Residue ILE  134 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue VAL  165 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue VAL  173 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue VAL  231 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue VAL  316 is missing expected H atoms. Skipping.
Evaluate side-chains
  173 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 1.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  119 MET cc_start: 0.9472 (tmm) cc_final: 0.8900 (tpt)
REVERT: K  150 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7426 (mm-30)
REVERT: K  215 HIS cc_start: 0.8655 (m-70) cc_final: 0.8313 (m90)
REVERT: K  241 CYS cc_start: 0.7568 (t) cc_final: 0.7248 (t)
REVERT: K  255 ASN cc_start: 0.7036 (m110) cc_final: 0.6603 (m110)
REVERT: K  259 MET cc_start: 0.8911 (mmm) cc_final: 0.8342 (tpp)
REVERT: K  278 ILE cc_start: 0.9560 (mt) cc_final: 0.9324 (tp)
REVERT: K  300 LYS cc_start: 0.9117 (mmmm) cc_final: 0.8889 (mmtp)
REVERT: A   35 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8139 (tm-30)
REVERT: A  101 ASN cc_start: 0.9344 (m-40) cc_final: 0.9006 (m-40)
REVERT: A  154 MET cc_start: 0.9091 (tpt) cc_final: 0.8847 (tpp)
REVERT: A  194 THR cc_start: 0.9161 (m) cc_final: 0.8878 (t)
REVERT: A  251 ASP cc_start: 0.8705 (t0) cc_final: 0.8171 (m-30)
REVERT: A  413 MET cc_start: 0.8499 (mmm) cc_final: 0.7847 (mmp)
REVERT: A  431 ASP cc_start: 0.8341 (m-30) cc_final: 0.8127 (m-30)
REVERT: H  105 LYS cc_start: 0.8883 (mtpt) cc_final: 0.8681 (mtpt)
REVERT: H  296 PHE cc_start: 0.7899 (m-80) cc_final: 0.7603 (m-80)
REVERT: H  384 ILE cc_start: 0.8648 (mm) cc_final: 0.8372 (mm)
REVERT: H  398 MET cc_start: 0.7833 (mmp) cc_final: 0.6995 (mtt)
REVERT: H  416 MET cc_start: 0.8676 (tpp) cc_final: 0.8431 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.3724
  time to fit residues: 92.2116
Evaluate side-chains
  146 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 1.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 23 optimal weight:   40.0000
   chunk 12 optimal weight:    6.9990
   chunk 74 optimal weight:   30.0000
   chunk 97 optimal weight:   20.0000
   chunk 71 optimal weight:    1.9990
   chunk 78 optimal weight:    8.9990
   chunk 32 optimal weight:   30.0000
   chunk 35 optimal weight:   20.0000
   chunk 38 optimal weight:    6.9990
   chunk 115 optimal weight:   30.0000
   overall best weight:    5.1388

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

Flipped N/Q/H residues before XYZ refinement:
K 149 ASN
K 266 ASN
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 380 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.085473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.061732 restraints weight = 56623.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.064507 restraints weight = 29180.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.066357 restraints weight = 19012.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.7388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9674  Z= 0.147
  Angle     :  0.508   7.222  13107  Z= 0.274
  Chirality :  0.041   0.168   1454
  Planarity :  0.004   0.061   1705
  Dihedral  :  8.962 165.401   1351
  Min Nonbonded Distance : 1.795

Molprobity Statistics.
  All-atom Clashscore : 45.89
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.20 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.25), residues: 1193
  helix:  1.27 (0.22), residues: 537
  sheet: -0.67 (0.37), residues: 215
  loop : -0.96 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 388 
 HIS   0.004   0.001   HIS A  88 
 PHE   0.010   0.001   PHE H 395 
 TYR   0.014   0.001   TYR H 224 
 ARG   0.011   0.001   ARG K 340 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03789 (  481)
  hydrogen bonds       : angle       4.85864 ( 1464)
  covalent geometry    : bond        0.00298 ( 9670)
  covalent geometry    : angle       0.50793 (13107)
  Misc. bond           : bond        0.00258 (    4)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE   17 is missing expected H atoms. Skipping.
Residue LEU   31 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue SER   45 is missing expected H atoms. Skipping.
Residue SER   54 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue VAL   60 is missing expected H atoms. Skipping.
Residue SER   70 is missing expected H atoms. Skipping.
Residue ILE   83 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  131 is missing expected H atoms. Skipping.
Residue ILE  134 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue VAL  165 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue VAL  173 is missing expected H atoms. Skipping.
Residue LYS  209 is missing expected H atoms. Skipping.
Residue VAL  231 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue VAL  316 is missing expected H atoms. Skipping.
Evaluate side-chains
  169 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 1.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  119 MET cc_start: 0.9470 (tmm) cc_final: 0.8994 (tpt)
REVERT: K  215 HIS cc_start: 0.8645 (m-70) cc_final: 0.8279 (m90)
REVERT: K  241 CYS cc_start: 0.7567 (t) cc_final: 0.7233 (t)
REVERT: K  255 ASN cc_start: 0.7001 (m110) cc_final: 0.6571 (m110)
REVERT: K  259 MET cc_start: 0.8923 (mmm) cc_final: 0.8345 (tpp)
REVERT: K  278 ILE cc_start: 0.9562 (mt) cc_final: 0.9332 (tp)
REVERT: A   35 GLN cc_start: 0.8339 (tm-30) cc_final: 0.8134 (tm-30)
REVERT: A  101 ASN cc_start: 0.9317 (m-40) cc_final: 0.8977 (m-40)
REVERT: A  154 MET cc_start: 0.9070 (tpt) cc_final: 0.8866 (tpp)
REVERT: A  194 THR cc_start: 0.9169 (m) cc_final: 0.8900 (t)
REVERT: A  251 ASP cc_start: 0.8676 (t0) cc_final: 0.8180 (m-30)
REVERT: A  413 MET cc_start: 0.8498 (mmm) cc_final: 0.7842 (mmp)
REVERT: A  431 ASP cc_start: 0.8328 (m-30) cc_final: 0.8099 (m-30)
REVERT: H   68 VAL cc_start: 0.8586 (t) cc_final: 0.8065 (t)
REVERT: H   93 VAL cc_start: 0.8004 (t) cc_final: 0.7747 (m)
REVERT: H  105 LYS cc_start: 0.8876 (mtpt) cc_final: 0.8672 (mtpt)
REVERT: H  398 MET cc_start: 0.7834 (mmp) cc_final: 0.7001 (mtt)
REVERT: H  416 MET cc_start: 0.8698 (tpp) cc_final: 0.8452 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.3044
  time to fit residues: 74.0857
Evaluate side-chains
  147 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 89 optimal weight:    8.9990
   chunk 50 optimal weight:    5.9990
   chunk 106 optimal weight:    7.9990
   chunk 27 optimal weight:   20.0000
   chunk 66 optimal weight:    8.9990
   chunk 63 optimal weight:    7.9990
   chunk 83 optimal weight:    1.9990
   chunk 112 optimal weight:    3.9990
   chunk 94 optimal weight:   20.0000
   chunk 60 optimal weight:   20.0000
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
K 133 GLN
K 266 ASN
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.085304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.061691 restraints weight = 56967.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.064466 restraints weight = 29460.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.066318 restraints weight = 19229.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.7528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9674  Z= 0.145
  Angle     :  0.504   6.754  13107  Z= 0.270
  Chirality :  0.040   0.156   1454
  Planarity :  0.004   0.044   1705
  Dihedral  :  8.813 164.987   1351
  Min Nonbonded Distance : 1.794

Molprobity Statistics.
  All-atom Clashscore : 46.16
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.11 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.25), residues: 1193
  helix:  1.30 (0.22), residues: 542
  sheet: -0.68 (0.36), residues: 215
  loop : -0.96 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  21 
 HIS   0.006   0.001   HIS H 266 
 PHE   0.014   0.001   PHE H 262 
 TYR   0.012   0.001   TYR H 435 
 ARG   0.009   0.001   ARG K 340 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03652 (  481)
  hydrogen bonds       : angle       4.80223 ( 1464)
  covalent geometry    : bond        0.00298 ( 9670)
  covalent geometry    : angle       0.50396 (13107)
  Misc. bond           : bond        0.00233 (    4)

===============================================================================
Job complete
usr+sys time: 4146.40 seconds
wall clock time: 74 minutes 56.10 seconds (4496.10 seconds total)