Starting phenix.real_space_refine
on Sat Aug 23 13:45:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7z2a_14459/08_2025/7z2a_14459.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7z2a_14459/08_2025/7z2a_14459.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7z2a_14459/08_2025/7z2a_14459.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7z2a_14459/08_2025/7z2a_14459.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7z2a_14459/08_2025/7z2a_14459.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7z2a_14459/08_2025/7z2a_14459.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.004 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      65      5.16       5
     C    5937      2.51       5
     N    1635      2.21       5
     O    1834      1.98       5
     H    2765      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12244
  Number of models: 1
  Model: ""
    Number of chains: 5
    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: "K"
      Number of atoms: 5494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 347, 5494
          Classifications: {'peptide': 347}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 337}
    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: 2.19, per 1000 atoms: 0.18
  Number of scatterers: 12244
  At special positions: 0
  Unit cell: (112.05, 105.3, 85.05, 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    1834      8.00
     N    1635      7.00
     C    5937      6.00
     H    2765      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: 0.91
  Conformation dependent library (CDL) restraints added in 395.2 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  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: 0.27
  Creating SS restraints...
    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: 3.609A  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: 3.523A  pdb=" N   ASN A 186 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   HIS A 192 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
      removed outlier: 3.957A  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: 4.407A  pdb=" N   SER A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 5.261A  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: 3.601A  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: 3.624A  pdb=" N   TRP A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LYS A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 411
      removed outlier: 4.079A  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: 4.428A  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: 4.487A  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: 3.995A  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: 3.603A  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: 3.811A  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: 5.739A  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: 3.604A  pdb=" N   GLN H 281 " --> pdb=" O   ARG H 278 " (cutoff:3.500A)
      removed outlier: 3.851A  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: 3.548A  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: 4.204A  pdb=" N   ARG H 401 " --> pdb=" O   ALA H 397 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 404 through 411
      removed outlier: 4.122A  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 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 sheet with id=AA1, 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: 6.249A  pdb=" N   PHE A  67 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 8.382A  pdb=" N   VAL A  66 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 7.792A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 6.137A  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: 3.875A  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: 3.850A  pdb=" N   SER A 165 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273
      removed outlier: 6.815A  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: 6.567A  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: 6.560A  pdb=" N   LEU A 378 " --> pdb=" O   CYS A 315 " (cutoff:3.500A)
      removed outlier: 4.542A  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=AA4, 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: 6.173A  pdb=" N   LEU H  67 " --> pdb=" O   VAL H  93 " (cutoff:3.500A)
      removed outlier: 8.472A  pdb=" N   ILE H  66 " --> pdb=" O   ILE H   4 " (cutoff:3.500A)
      removed outlier: 6.722A  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: 5.856A  pdb=" N   GLU H   3 " --> pdb=" O   LEU H 132 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLY H 134 " --> pdb=" O   GLU H   3 " (cutoff:3.500A)
      removed outlier: 4.922A  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: 8.090A  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: 6.417A  pdb=" N   LEU H 137 " --> pdb=" O   PHE H 169 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   VAL H 171 " --> pdb=" O   LEU H 137 " (cutoff:3.500A)
      removed outlier: 7.217A  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: 6.826A  pdb=" N   THR H 168 " --> pdb=" O   TYR H 202 " (cutoff:3.500A)
      removed outlier: 7.225A  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: 7.418A  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: 5.067A  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: 6.572A  pdb=" N   THR H 376 " --> pdb=" O   ALA H 317 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   ALA H 317 " --> pdb=" O   THR H 376 " (cutoff:3.500A)
      removed outlier: 6.606A  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: 6.915A  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: 6.549A  pdb=" N   VAL H 315 " --> pdb=" O   LYS H 352 " (cutoff:3.500A)
      removed outlier: 8.140A  pdb=" N   ALA H 354 " --> pdb=" O   VAL H 315 " (cutoff:3.500A)
      removed outlier: 6.413A  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: 3.586A  pdb=" N   LEU H 248 " --> pdb=" O   VAL H 355 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 53 through 56
      removed outlier: 3.891A  pdb=" N   LYS H  60 " --> pdb=" O   ALA H  56 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'K' and resid 63 through 65
      removed outlier: 9.069A  pdb=" N   TYR K  63 " --> pdb=" O   MET K   6 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL K   8 " --> pdb=" O   TYR K  63 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   PHE K  65 " --> pdb=" O   VAL K   8 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   ILE K  10 " --> pdb=" O   PHE K  65 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   THR K  93 " --> pdb=" O   LEU K 316 " (cutoff:3.500A)
      removed outlier: 7.432A  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: 7.384A  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: 6.355A  pdb=" N   SER K  92 " --> pdb=" O   CYS K 241 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   ILE K 243 " --> pdb=" O   SER K  92 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   VAL K  94 " --> pdb=" O   ILE K 243 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'K' and resid 63 through 65
      removed outlier: 9.069A  pdb=" N   TYR K  63 " --> pdb=" O   MET K   6 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL K   8 " --> pdb=" O   TYR K  63 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   PHE K  65 " --> pdb=" O   VAL K   8 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   ILE K  10 " --> pdb=" O   PHE K  65 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   THR K  93 " --> pdb=" O   LEU K 316 " (cutoff:3.500A)
      removed outlier: 7.432A  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: 7.384A  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: 6.355A  pdb=" N   SER K  92 " --> pdb=" O   CYS K 241 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   ILE K 243 " --> pdb=" O   SER K  92 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   VAL K  94 " --> pdb=" O   ILE K 243 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'K' and resid 28 through 32
      removed outlier: 6.536A  pdb=" N   MET K  35 " --> pdb=" O   MET K  31 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'K' and resid 165 through 167
    Processing sheet with id=AB1, first strand: chain 'K' and resid 202 through 205
      removed outlier: 4.981A  pdb=" N   GLU K 203 " --> pdb=" O   THR K 210 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   THR K 210 " --> pdb=" O   GLU K 203 " (cutoff:3.500A)

    510 hydrogen bonds defined for protein.
    1461 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.79

  Time building geometry restraints manager: 1.16 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: 2758
        1.13 -     1.31: 1625
        1.31 -     1.48: 3888
        1.48 -     1.66: 4056
        1.66 -     1.83: 105
  Bond restraints: 12432
  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  58 "
       pdb="HH11 ARG K  58 "
    ideal  model  delta    sigma   weight residual
    0.860  1.045 -0.185 2.00e-02 2.50e+03 8.54e+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 8.44e+01
  bond pdb=" NH2 ARG K  58 "
       pdb="HH21 ARG K  58 "
    ideal  model  delta    sigma   weight residual
    0.860  1.039 -0.179 2.00e-02 2.50e+03 7.97e+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 7.83e+01
  ... (remaining 12427 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.07: 17867
        3.07 -     6.14: 1276
        6.14 -     9.21: 218
        9.21 -    12.28: 15
       12.28 -    15.35: 8
  Bond angle restraints: 19384
  Sorted by residual:
  angle pdb=" C   LYS K 139 "
        pdb=" N   ILE K 140 "
        pdb=" CA  ILE K 140 "
      ideal   model   delta    sigma   weight residual
     122.48  113.87    8.61 1.25e+00 6.40e-01 4.75e+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  126.71   -6.84 1.04e+00 9.25e-01 4.33e+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  100.91   10.12 1.54e+00 4.22e-01 4.32e+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  126.20   -6.38 9.80e-01 1.04e+00 4.23e+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  117.01   -9.21 1.45e+00 4.76e-01 4.03e+01
  ... (remaining 19379 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.62: 6526
       33.62 -    67.24: 153
       67.24 -   100.86: 17
      100.86 -   134.48: 0
      134.48 -   168.09: 3
  Dihedral angle restraints: 6699
    sinusoidal: 3112
      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 -136.41  -43.59     0      5.00e+00 4.00e-02 7.60e+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 -122.64 -168.09     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  -51.70  156.29     1      2.00e+01 2.50e-03 4.60e+01
  ... (remaining 6696 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 989
       0.079 -    0.159: 343
       0.159 -    0.238: 97
       0.238 -    0.317: 22
       0.317 -    0.396: 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    2.11    0.40 2.00e-01 2.50e+01 3.92e+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
  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 2.69e+00
  ... (remaining 1451 not shown)

  Planarity restraints: 2040
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS K 332 "    0.153 2.00e-02 2.50e+03   1.62e-01 5.90e+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 "   -0.041 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 "   -0.381 2.00e-02 2.50e+03
        pdb=" HD2 HIS K 332 "   -0.123 2.00e-02 2.50e+03
        pdb=" HE1 HIS K 332 "    0.121 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   2.85e-02 2.44e+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 "    0.025 2.00e-02 2.50e+03
        pdb=" CE1 TYR K   4 "    0.012 2.00e-02 2.50e+03
        pdb=" CE2 TYR K   4 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  TYR K   4 "   -0.007 2.00e-02 2.50e+03
        pdb=" OH  TYR K   4 "   -0.048 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 2.34e+01
        pdb=" CG  TYR K  75 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD1 TYR K  75 "   -0.028 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 "    0.038 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 2037 not shown)

  Histogram of nonbonded interaction distances:
        0.27 -     1.13: 8
        1.13 -     2.00: 263
        2.00 -     2.87: 15664
        2.87 -     3.73: 39212
        3.73 -     4.60: 69387
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 124534
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 431 "
            pdb="HG11 VAL K  48 "
     model   vdw
     0.268 2.620
  nonbonded pdb=" CG  GLU A 415 "
            pdb="HH12 ARG K 340 "
     model   vdw
     0.813 2.200
  nonbonded pdb=" OD1 ASP A 431 "
            pdb=" CG1 VAL K  48 "
     model   vdw
     0.925 3.100
  nonbonded pdb=" OE1 GLU A 434 "
            pdb=" OE1 GLN K  51 "
     model   vdw
     0.946 2.800
  nonbonded pdb=" OE2 GLU H 431 "
            pdb=" HD2 PHE K 293 "
     model   vdw
     1.011 2.450
  ... (remaining 124529 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:             0.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.110
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     10.520
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6482
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      :  0.013   0.313   9671  Z= 0.860
  Angle     :  1.594  14.069  13103  Z= 1.079
  Chirality :  0.089   0.396   1454
  Planarity :  0.008   0.074   1703
  Dihedral  : 14.753 168.095   3606
  Min Nonbonded Distance : 0.925

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.85 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  5.03 %
    Favored  : 94.49 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.00 (0.23), residues: 1193
  helix:  0.65 (0.20), residues: 518
  sheet: -0.23 (0.36), residues: 209
  loop : -0.49 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K 260 
 TYR   0.064   0.006   TYR K   4 
 PHE   0.033   0.004   PHE K 179 
 TRP   0.017   0.003   TRP A  21 
 HIS   0.014   0.002   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.01205 ( 9667)
  covalent geometry    : angle       1.59422 (13103)
  hydrogen bonds       : bond        0.18695 (  481)
  hydrogen bonds       : angle       7.60444 ( 1461)
  Misc. bond           : bond        0.23315 (    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
****************************
Evaluate side-chains
  259 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 254
  time to evaluate  : 0.248 
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: A  205 ASP cc_start: 0.5696 (t0) cc_final: 0.5138 (t0)
REVERT: A  210 TYR cc_start: 0.8635 (m-80) cc_final: 0.8200 (m-10)
REVERT: A  295 CYS cc_start: 0.7822 (m) cc_final: 0.7319 (m)
REVERT: A  380 ASN cc_start: 0.6409 (t0) cc_final: 0.5939 (t0)
REVERT: H   20 PHE cc_start: 0.7661 (t80) cc_final: 0.7383 (t80)
REVERT: H   75 MET cc_start: 0.7827 (mmp) cc_final: 0.7615 (mmp)
REVERT: H  156 LYS cc_start: 0.9195 (mmtm) cc_final: 0.8667 (mtmt)
REVERT: K  215 HIS cc_start: 0.5900 (m-70) cc_final: 0.5135 (m-70)
  outliers start: 5
  outliers final: 1
  residues processed: 258
  average time/residue: 0.1122
  time to fit residues: 39.6363
Evaluate side-chains
  128 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:   20.0000
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    8.9990
   chunk 117 optimal weight:    7.9990
   overall best weight:    7.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 101 ASN
A 226 ASN
A 300 ASN
A 406 HIS
H  11 GLN
H  15 GLN
H  28 HIS
H  37 HIS
** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 197 ASN
** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 406 HIS
** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.073758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.052910 restraints weight = 70240.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.055391 restraints weight = 37031.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.057005 restraints weight = 23895.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.058097 restraints weight = 17708.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.058730 restraints weight = 14423.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.3798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9671  Z= 0.232
  Angle     :  0.694   7.538  13103  Z= 0.376
  Chirality :  0.043   0.174   1454
  Planarity :  0.005   0.077   1703
  Dihedral  : 10.551 175.897   1350
  Min Nonbonded Distance : 1.803

Molprobity Statistics.
  All-atom Clashscore : 30.53
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.51 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.55 %
    Favored  : 98.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.24), residues: 1193
  helix:  1.26 (0.21), residues: 532
  sheet:  0.11 (0.36), residues: 208
  loop : -0.45 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K 340 
 TYR   0.022   0.002   TYR K  75 
 PHE   0.025   0.002   PHE K 144 
 TRP   0.009   0.001   TRP H 407 
 HIS   0.008   0.002   HIS K 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 9667)
  covalent geometry    : angle       0.69420 (13103)
  hydrogen bonds       : bond        0.05251 (  481)
  hydrogen bonds       : angle       5.61769 ( 1461)
  Misc. bond           : bond        0.00210 (    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
****************************
Evaluate side-chains
  156 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 155
  time to evaluate  : 0.279 
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: A  109 THR cc_start: 0.9053 (m) cc_final: 0.8516 (p)
REVERT: A  205 ASP cc_start: 0.7365 (t0) cc_final: 0.6981 (t0)
REVERT: A  302 MET cc_start: 0.9373 (mmp) cc_final: 0.9086 (mpp)
REVERT: A  351 PHE cc_start: 0.7663 (m-80) cc_final: 0.7241 (m-80)
REVERT: H   37 HIS cc_start: 0.8547 (m-70) cc_final: 0.8328 (m-70)
REVERT: H  160 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8264 (mt-10)
REVERT: H  267 PHE cc_start: 0.8942 (m-80) cc_final: 0.8710 (m-80)
REVERT: H  295 MET cc_start: 0.8898 (ptp) cc_final: 0.8492 (ttm)
REVERT: H  302 MET cc_start: 0.7774 (mtm) cc_final: 0.6960 (mtt)
REVERT: H  325 MET cc_start: 0.8260 (mmt) cc_final: 0.7841 (mmm)
REVERT: H  342 TYR cc_start: 0.8151 (m-10) cc_final: 0.7879 (m-10)
REVERT: K  144 PHE cc_start: 0.8981 (t80) cc_final: 0.8224 (t80)
REVERT: K  215 HIS cc_start: 0.9069 (m-70) cc_final: 0.8380 (m-70)
  outliers start: 1
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1186
  time to fit residues: 25.3326
Evaluate side-chains
  109 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 14 optimal weight:   20.0000
   chunk 15 optimal weight:    9.9990
   chunk 64 optimal weight:    2.9990
   chunk 68 optimal weight:   30.0000
   chunk 29 optimal weight:   10.0000
   chunk 90 optimal weight:   20.0000
   chunk 31 optimal weight:    0.0050
   chunk 76 optimal weight:   10.0000
   chunk 3 optimal weight:   20.0000
   chunk 85 optimal weight:    5.9990
   overall best weight:    4.0000

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

Flipped N/Q/H residues before XYZ refinement:
A  61 HIS
A 228 ASN
H  14 ASN
** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K   5 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.072738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.051815 restraints weight = 70780.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.054177 restraints weight = 37115.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.055734 restraints weight = 24075.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.056771 restraints weight = 17890.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.057446 restraints weight = 14658.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.4500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.095   9671  Z= 0.164
  Angle     :  0.596  14.663  13103  Z= 0.323
  Chirality :  0.041   0.172   1454
  Planarity :  0.006   0.172   1703
  Dihedral  : 11.177 179.645   1350
  Min Nonbonded Distance : 1.816

Molprobity Statistics.
  All-atom Clashscore : 34.26
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.10 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.25), residues: 1193
  helix:  1.69 (0.22), residues: 529
  sheet: -0.20 (0.35), residues: 221
  loop : -0.31 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.031   0.001   ARG K 297 
 TYR   0.018   0.001   TYR K  75 
 PHE   0.014   0.001   PHE K 293 
 TRP   0.014   0.001   TRP H  21 
 HIS   0.007   0.001   HIS H 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9667)
  covalent geometry    : angle       0.59589 (13103)
  hydrogen bonds       : bond        0.04867 (  481)
  hydrogen bonds       : angle       5.24144 ( 1461)
  Misc. bond           : bond        0.00346 (    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
****************************
Evaluate side-chains
  142 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.296 
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: A   52 PHE cc_start: 0.8538 (m-80) cc_final: 0.8317 (m-80)
REVERT: A   76 ASP cc_start: 0.8744 (t70) cc_final: 0.8276 (t0)
REVERT: A  109 THR cc_start: 0.8658 (m) cc_final: 0.8236 (p)
REVERT: A  136 LEU cc_start: 0.9156 (mp) cc_final: 0.8718 (mp)
REVERT: A  205 ASP cc_start: 0.7572 (t0) cc_final: 0.7169 (t0)
REVERT: A  302 MET cc_start: 0.9269 (mmp) cc_final: 0.8989 (mmt)
REVERT: A  317 LEU cc_start: 0.8923 (mm) cc_final: 0.8690 (mp)
REVERT: A  351 PHE cc_start: 0.7747 (m-80) cc_final: 0.7031 (m-80)
REVERT: H   14 ASN cc_start: 0.8837 (m110) cc_final: 0.8605 (t0)
REVERT: H   37 HIS cc_start: 0.8524 (m-70) cc_final: 0.8297 (m-70)
REVERT: H  230 LEU cc_start: 0.9491 (tp) cc_final: 0.9267 (tp)
REVERT: H  325 MET cc_start: 0.8202 (mmt) cc_final: 0.7598 (mmm)
REVERT: H  372 LYS cc_start: 0.8843 (mptt) cc_final: 0.8526 (mmtm)
REVERT: K    6 MET cc_start: 0.5897 (tpp) cc_final: 0.5573 (tpp)
REVERT: K  144 PHE cc_start: 0.8937 (t80) cc_final: 0.8159 (t80)
REVERT: K  190 MET cc_start: 0.9216 (tmm) cc_final: 0.8826 (tmm)
REVERT: K  215 HIS cc_start: 0.9062 (m-70) cc_final: 0.8742 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1012
  time to fit residues: 20.5212
Evaluate side-chains
  103 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 73 optimal weight:   20.0000
   chunk 30 optimal weight:    5.9990
   chunk 14 optimal weight:    8.9990
   chunk 81 optimal weight:   40.0000
   chunk 67 optimal weight:    0.9980
   chunk 16 optimal weight:    0.3980
   chunk 60 optimal weight:    7.9990
   chunk 25 optimal weight:    7.9990
   chunk 69 optimal weight:    0.6980
   chunk 31 optimal weight:   10.0000
   chunk 82 optimal weight:    5.9990
   overall best weight:    2.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 192 HIS
** H   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 247 GLN
** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 349 ASN
** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 433 GLN ** 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 = 0.3716 r_free = 0.3716 target = 0.072319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.051607 restraints weight = 69316.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.053937 restraints weight = 36396.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.055494 restraints weight = 23584.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.056469 restraints weight = 17464.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.057160 restraints weight = 14339.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.5046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9671  Z= 0.122
  Angle     :  0.512   6.587  13103  Z= 0.276
  Chirality :  0.040   0.184   1454
  Planarity :  0.010   0.391   1703
  Dihedral  : 10.703 178.456   1350
  Min Nonbonded Distance : 1.848

Molprobity Statistics.
  All-atom Clashscore : 35.70
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.93 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.45 %
    Favored  : 98.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.25), residues: 1193
  helix:  1.84 (0.23), residues: 529
  sheet: -0.24 (0.36), residues: 211
  loop : -0.18 (0.31), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG K 297 
 TYR   0.016   0.001   TYR H 432 
 PHE   0.014   0.001   PHE H 135 
 TRP   0.010   0.001   TRP H  21 
 HIS   0.008   0.001   HIS H 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 9667)
  covalent geometry    : angle       0.51175 (13103)
  hydrogen bonds       : bond        0.04141 (  481)
  hydrogen bonds       : angle       5.00509 ( 1461)
  Misc. bond           : bond        0.00373 (    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
****************************
Evaluate side-chains
  138 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.245 
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: A   76 ASP cc_start: 0.8717 (t70) cc_final: 0.8205 (t0)
REVERT: A  109 THR cc_start: 0.8739 (m) cc_final: 0.8421 (p)
REVERT: A  205 ASP cc_start: 0.7546 (t0) cc_final: 0.7078 (t70)
REVERT: A  302 MET cc_start: 0.9286 (mmp) cc_final: 0.9026 (mmt)
REVERT: A  351 PHE cc_start: 0.7791 (m-80) cc_final: 0.7088 (m-80)
REVERT: H   37 HIS cc_start: 0.8489 (m-70) cc_final: 0.8275 (m-70)
REVERT: H  160 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8212 (mt-10)
REVERT: H  181 VAL cc_start: 0.8898 (t) cc_final: 0.8679 (p)
REVERT: H  372 LYS cc_start: 0.8804 (mptt) cc_final: 0.8522 (mmtm)
REVERT: H  413 MET cc_start: 0.8312 (mmt) cc_final: 0.7018 (mmt)
REVERT: K  144 PHE cc_start: 0.8893 (t80) cc_final: 0.8165 (t80)
REVERT: K  190 MET cc_start: 0.9227 (tmm) cc_final: 0.8834 (tmm)
REVERT: K  215 HIS cc_start: 0.9050 (m-70) cc_final: 0.8757 (m-70)
  outliers start: 1
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0920
  time to fit residues: 18.9707
Evaluate side-chains
  105 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 97 optimal weight:   30.0000
   chunk 104 optimal weight:    9.9990
   chunk 57 optimal weight:    8.9990
   chunk 93 optimal weight:   30.0000
   chunk 117 optimal weight:   20.0000
   chunk 105 optimal weight:   30.0000
   chunk 96 optimal weight:    5.9990
   chunk 21 optimal weight:   20.0000
   chunk 75 optimal weight:    5.9990
   chunk 55 optimal weight:    9.9990
   chunk 12 optimal weight:   20.0000
   overall best weight:    8.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 192 HIS
** H   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  11 GLN
** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 433 GLN ** 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 = 0.3618 r_free = 0.3618 target = 0.068128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.047647 restraints weight = 73276.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.049808 restraints weight = 38625.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.051220 restraints weight = 25006.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.052162 restraints weight = 18589.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.052775 restraints weight = 15265.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.5779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9671  Z= 0.229
  Angle     :  0.604   8.958  13103  Z= 0.322
  Chirality :  0.041   0.141   1454
  Planarity :  0.009   0.348   1703
  Dihedral  : 10.744 178.168   1350
  Min Nonbonded Distance : 1.732

Molprobity Statistics.
  All-atom Clashscore : 43.82
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.35 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.03 %
    Favored  : 97.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.25), residues: 1193
  helix:  1.46 (0.23), residues: 539
  sheet: -0.51 (0.36), residues: 203
  loop : -0.27 (0.31), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K 297 
 TYR   0.017   0.002   TYR K  75 
 PHE   0.020   0.002   PHE H 169 
 TRP   0.007   0.001   TRP H 407 
 HIS   0.010   0.002   HIS H   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 9667)
  covalent geometry    : angle       0.60363 (13103)
  hydrogen bonds       : bond        0.04175 (  481)
  hydrogen bonds       : angle       5.17488 ( 1461)
  Misc. bond           : bond        0.00299 (    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
****************************
Evaluate side-chains
  128 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.415 
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: A   76 ASP cc_start: 0.8917 (t70) cc_final: 0.8407 (t0)
REVERT: A  109 THR cc_start: 0.8842 (m) cc_final: 0.8488 (p)
REVERT: A  118 VAL cc_start: 0.9613 (m) cc_final: 0.9331 (p)
REVERT: A  302 MET cc_start: 0.9420 (mmp) cc_final: 0.8773 (mpp)
REVERT: H   37 HIS cc_start: 0.8734 (m-70) cc_final: 0.8445 (m-70)
REVERT: H   50 ASN cc_start: 0.8685 (p0) cc_final: 0.8395 (p0)
REVERT: H  295 MET cc_start: 0.8658 (ttm) cc_final: 0.8251 (ttm)
REVERT: H  372 LYS cc_start: 0.8903 (mptt) cc_final: 0.8663 (mmtm)
REVERT: K  144 PHE cc_start: 0.9012 (t80) cc_final: 0.8268 (t80)
REVERT: K  190 MET cc_start: 0.9311 (tmm) cc_final: 0.8949 (tmm)
REVERT: K  215 HIS cc_start: 0.9187 (m-70) cc_final: 0.8105 (m-70)
  outliers start: 1
  outliers final: 1
  residues processed: 128
  average time/residue: 0.0944
  time to fit residues: 17.9586
Evaluate side-chains
  94 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 99 optimal weight:   30.0000
   chunk 109 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 5 optimal weight:   20.0000
   chunk 20 optimal weight:    0.9980
   chunk 83 optimal weight:   30.0000
   chunk 75 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 95 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 433 GLN ** 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 = 0.3631 r_free = 0.3631 target = 0.068433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.048378 restraints weight = 71605.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.050548 restraints weight = 37266.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.051928 restraints weight = 23877.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.052860 restraints weight = 17740.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.053437 restraints weight = 14574.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.6037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9671  Z= 0.138
  Angle     :  0.502   6.720  13103  Z= 0.270
  Chirality :  0.039   0.136   1454
  Planarity :  0.009   0.346   1703
  Dihedral  : 10.824 179.453   1350
  Min Nonbonded Distance : 1.796

Molprobity Statistics.
  All-atom Clashscore : 42.06
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.19 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.25), residues: 1193
  helix:  1.72 (0.23), residues: 535
  sheet: -0.48 (0.36), residues: 205
  loop : -0.22 (0.31), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K 297 
 TYR   0.016   0.001   TYR A 357 
 PHE   0.013   0.001   PHE K 144 
 TRP   0.012   0.001   TRP H  21 
 HIS   0.005   0.001   HIS H  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9667)
  covalent geometry    : angle       0.50191 (13103)
  hydrogen bonds       : bond        0.03741 (  481)
  hydrogen bonds       : angle       4.90335 ( 1461)
  Misc. bond           : bond        0.00263 (    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
****************************
Evaluate side-chains
  122 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.298 
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: A   76 ASP cc_start: 0.8856 (t70) cc_final: 0.8292 (t0)
REVERT: A  109 THR cc_start: 0.8788 (m) cc_final: 0.8447 (p)
REVERT: A  118 VAL cc_start: 0.9601 (m) cc_final: 0.9315 (p)
REVERT: A  302 MET cc_start: 0.9444 (mmp) cc_final: 0.8851 (mpp)
REVERT: A  351 PHE cc_start: 0.7390 (m-80) cc_final: 0.6901 (m-80)
REVERT: H   37 HIS cc_start: 0.8751 (m-70) cc_final: 0.8486 (m-70)
REVERT: H   50 ASN cc_start: 0.8714 (p0) cc_final: 0.8406 (p0)
REVERT: H  290 GLU cc_start: 0.7962 (tp30) cc_final: 0.7658 (tp30)
REVERT: H  295 MET cc_start: 0.8545 (ttm) cc_final: 0.8109 (ttm)
REVERT: H  323 MET cc_start: 0.6735 (mtm) cc_final: 0.6058 (mtt)
REVERT: H  372 LYS cc_start: 0.8959 (mptt) cc_final: 0.8735 (mmtm)
REVERT: H  413 MET cc_start: 0.7874 (mmt) cc_final: 0.6643 (mmt)
REVERT: K  144 PHE cc_start: 0.8986 (t80) cc_final: 0.8273 (t80)
REVERT: K  190 MET cc_start: 0.9322 (tmm) cc_final: 0.8951 (tmm)
REVERT: K  215 HIS cc_start: 0.9233 (m-70) cc_final: 0.8075 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1003
  time to fit residues: 17.8135
Evaluate side-chains
  92 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 86 optimal weight:   20.0000
   chunk 20 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   chunk 23 optimal weight:    0.8980
   chunk 108 optimal weight:   40.0000
   chunk 40 optimal weight:    1.9990
   chunk 41 optimal weight:   20.0000
   chunk 68 optimal weight:   20.0000
   chunk 81 optimal weight:    5.9990
   chunk 26 optimal weight:   30.0000
   chunk 30 optimal weight:    9.9990
   overall best weight:    4.5788

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  11 GLN
** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 433 GLN ** 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 = 0.3620 r_free = 0.3620 target = 0.067763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.047720 restraints weight = 71678.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.049929 restraints weight = 35893.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.051376 restraints weight = 22588.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.052320 restraints weight = 16523.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.052917 restraints weight = 13450.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.6355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9671  Z= 0.143
  Angle     :  0.495   6.860  13103  Z= 0.263
  Chirality :  0.039   0.137   1454
  Planarity :  0.008   0.307   1703
  Dihedral  : 10.847 178.821   1350
  Min Nonbonded Distance : 1.782

Molprobity Statistics.
  All-atom Clashscore : 43.76
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.44 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.26), residues: 1193
  helix:  1.91 (0.23), residues: 530
  sheet: -0.43 (0.37), residues: 203
  loop : -0.20 (0.31), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K 297 
 TYR   0.012   0.001   TYR K  75 
 PHE   0.013   0.001   PHE K 144 
 TRP   0.007   0.001   TRP H 407 
 HIS   0.004   0.001   HIS H  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9667)
  covalent geometry    : angle       0.49537 (13103)
  hydrogen bonds       : bond        0.03561 (  481)
  hydrogen bonds       : angle       4.77149 ( 1461)
  Misc. bond           : bond        0.00263 (    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
****************************
Evaluate side-chains
  124 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.333 
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: A   76 ASP cc_start: 0.8676 (t70) cc_final: 0.8185 (t0)
REVERT: A  109 THR cc_start: 0.8852 (m) cc_final: 0.8557 (p)
REVERT: A  118 VAL cc_start: 0.9586 (m) cc_final: 0.9256 (p)
REVERT: A  230 LEU cc_start: 0.9551 (tt) cc_final: 0.9327 (mm)
REVERT: A  302 MET cc_start: 0.9474 (mmp) cc_final: 0.8861 (mpp)
REVERT: H  295 MET cc_start: 0.8497 (ttm) cc_final: 0.8175 (ttm)
REVERT: H  323 MET cc_start: 0.6305 (mtm) cc_final: 0.6065 (mtt)
REVERT: K  144 PHE cc_start: 0.8925 (t80) cc_final: 0.8270 (t80)
REVERT: K  153 CYS cc_start: 0.8916 (t) cc_final: 0.8561 (m)
REVERT: K  215 HIS cc_start: 0.9144 (m-70) cc_final: 0.7954 (m-70)
REVERT: K  261 MET cc_start: 0.9049 (mtp) cc_final: 0.8848 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.0896
  time to fit residues: 16.2922
Evaluate side-chains
  99 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 112 optimal weight:   30.0000
   chunk 96 optimal weight:   30.0000
   chunk 30 optimal weight:   20.0000
   chunk 94 optimal weight:   30.0000
   chunk 16 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   chunk 83 optimal weight:   20.0000
   chunk 81 optimal weight:    6.9990
   chunk 24 optimal weight:    6.9990
   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 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 433 GLN ** 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 = 0.3600 r_free = 0.3600 target = 0.066762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.046930 restraints weight = 71536.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.049098 restraints weight = 35637.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.050525 restraints weight = 22443.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.051441 restraints weight = 16437.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.051950 restraints weight = 13431.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.6643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9671  Z= 0.174
  Angle     :  0.517   6.424  13103  Z= 0.277
  Chirality :  0.040   0.143   1454
  Planarity :  0.008   0.301   1703
  Dihedral  : 11.018 178.423   1350
  Min Nonbonded Distance : 1.807

Molprobity Statistics.
  All-atom Clashscore : 46.11
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.27 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.26), residues: 1193
  helix:  1.89 (0.23), residues: 525
  sheet: -0.56 (0.37), residues: 207
  loop : -0.32 (0.31), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K 297 
 TYR   0.013   0.001   TYR K  75 
 PHE   0.012   0.002   PHE H 268 
 TRP   0.007   0.001   TRP H 407 
 HIS   0.004   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9667)
  covalent geometry    : angle       0.51665 (13103)
  hydrogen bonds       : bond        0.03602 (  481)
  hydrogen bonds       : angle       4.83380 ( 1461)
  Misc. bond           : bond        0.00265 (    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
****************************
Evaluate side-chains
  120 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.317 
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: A   76 ASP cc_start: 0.8698 (t70) cc_final: 0.8188 (t0)
REVERT: A  109 THR cc_start: 0.8702 (m) cc_final: 0.8430 (p)
REVERT: A  118 VAL cc_start: 0.9598 (m) cc_final: 0.9264 (p)
REVERT: A  245 ASP cc_start: 0.7990 (p0) cc_final: 0.7556 (p0)
REVERT: A  302 MET cc_start: 0.9456 (mmp) cc_final: 0.8904 (mpp)
REVERT: H  290 GLU cc_start: 0.7849 (tp30) cc_final: 0.7508 (tp30)
REVERT: H  295 MET cc_start: 0.8430 (ttm) cc_final: 0.8178 (ttm)
REVERT: H  309 HIS cc_start: 0.9179 (m-70) cc_final: 0.8976 (m-70)
REVERT: H  413 MET cc_start: 0.7608 (mmt) cc_final: 0.7035 (mmp)
REVERT: K  144 PHE cc_start: 0.8992 (t80) cc_final: 0.8355 (t80)
REVERT: K  153 CYS cc_start: 0.8949 (t) cc_final: 0.8598 (m)
REVERT: K  215 HIS cc_start: 0.9211 (m-70) cc_final: 0.8321 (m-70)
REVERT: K  293 PHE cc_start: 0.6716 (t80) cc_final: 0.6505 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.0993
  time to fit residues: 17.3041
Evaluate side-chains
  96 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 9 optimal weight:    8.9990
   chunk 89 optimal weight:   40.0000
   chunk 117 optimal weight:   20.0000
   chunk 61 optimal weight:   20.0000
   chunk 57 optimal weight:   10.0000
   chunk 100 optimal weight:   30.0000
   chunk 5 optimal weight:    6.9990
   chunk 103 optimal weight:   30.0000
   chunk 48 optimal weight:   10.0000
   chunk 50 optimal weight:    5.9990
   chunk 17 optimal weight:    0.5980
   overall best weight:    6.5190

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

Flipped N/Q/H residues before XYZ refinement:
A 128 GLN
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 433 GLN ** 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 = 0.3579 r_free = 0.3579 target = 0.066380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.046262 restraints weight = 72330.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.048404 restraints weight = 36252.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.049734 restraints weight = 22992.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.050680 restraints weight = 17142.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.051250 restraints weight = 13987.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.6930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9671  Z= 0.175
  Angle     :  0.529   9.177  13103  Z= 0.281
  Chirality :  0.039   0.141   1454
  Planarity :  0.008   0.282   1703
  Dihedral  : 10.980 178.515   1350
  Min Nonbonded Distance : 1.807

Molprobity Statistics.
  All-atom Clashscore : 47.29
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.02 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.25), residues: 1193
  helix:  1.80 (0.23), residues: 525
  sheet: -0.75 (0.37), residues: 195
  loop : -0.49 (0.30), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K 297 
 TYR   0.015   0.001   TYR K  75 
 PHE   0.012   0.001   PHE H 169 
 TRP   0.010   0.001   TRP H  21 
 HIS   0.004   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9667)
  covalent geometry    : angle       0.52932 (13103)
  hydrogen bonds       : bond        0.03599 (  481)
  hydrogen bonds       : angle       4.85034 ( 1461)
  Misc. bond           : bond        0.00264 (    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
****************************
Evaluate side-chains
  114 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.269 
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: A   76 ASP cc_start: 0.8735 (t70) cc_final: 0.8221 (t0)
REVERT: A  109 THR cc_start: 0.8923 (m) cc_final: 0.8618 (p)
REVERT: A  118 VAL cc_start: 0.9559 (m) cc_final: 0.9262 (p)
REVERT: A  245 ASP cc_start: 0.8044 (p0) cc_final: 0.7650 (p0)
REVERT: A  267 PHE cc_start: 0.9028 (m-80) cc_final: 0.8683 (m-10)
REVERT: A  302 MET cc_start: 0.9472 (mmp) cc_final: 0.8880 (mpp)
REVERT: H  259 MET cc_start: 0.9057 (mmp) cc_final: 0.8787 (mmp)
REVERT: H  290 GLU cc_start: 0.7854 (tp30) cc_final: 0.7588 (tp30)
REVERT: H  295 MET cc_start: 0.8466 (ttm) cc_final: 0.8201 (ttm)
REVERT: H  309 HIS cc_start: 0.9227 (m-70) cc_final: 0.9022 (m-70)
REVERT: H  413 MET cc_start: 0.7847 (mmt) cc_final: 0.6901 (mmt)
REVERT: K  144 PHE cc_start: 0.9006 (t80) cc_final: 0.8369 (t80)
REVERT: K  153 CYS cc_start: 0.8938 (t) cc_final: 0.8597 (m)
REVERT: K  215 HIS cc_start: 0.9248 (m-70) cc_final: 0.8423 (m-70)
REVERT: K  293 PHE cc_start: 0.6977 (t80) cc_final: 0.6749 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0927
  time to fit residues: 15.5298
Evaluate side-chains
  95 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 86 optimal weight:   20.0000
   chunk 31 optimal weight:   10.0000
   chunk 46 optimal weight:    8.9990
   chunk 71 optimal weight:   20.0000
   chunk 24 optimal weight:    7.9990
   chunk 116 optimal weight:   20.0000
   chunk 77 optimal weight:    9.9990
   chunk 35 optimal weight:   10.0000
   chunk 83 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 197 HIS
** H   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 433 GLN ** 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 = 0.3567 r_free = 0.3567 target = 0.065987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.046110 restraints weight = 72556.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.048238 restraints weight = 35710.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.049676 restraints weight = 22548.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.050557 restraints weight = 16450.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.051136 restraints weight = 13486.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.7109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9671  Z= 0.190
  Angle     :  0.540   7.756  13103  Z= 0.289
  Chirality :  0.039   0.141   1454
  Planarity :  0.011   0.447   1703
  Dihedral  : 10.534 175.181   1350
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 48.89
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.27 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.25), residues: 1193
  helix:  1.65 (0.23), residues: 531
  sheet: -0.82 (0.37), residues: 191
  loop : -0.64 (0.30), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 297 
 TYR   0.022   0.002   TYR K   4 
 PHE   0.032   0.002   PHE K 293 
 TRP   0.009   0.001   TRP H  21 
 HIS   0.005   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 9667)
  covalent geometry    : angle       0.53993 (13103)
  hydrogen bonds       : bond        0.03729 (  481)
  hydrogen bonds       : angle       4.88682 ( 1461)
  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
****************************
Evaluate side-chains
  109 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.398 
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: A   71 GLU cc_start: 0.6815 (mp0) cc_final: 0.6496 (mp0)
REVERT: A   76 ASP cc_start: 0.8769 (t70) cc_final: 0.8253 (t0)
REVERT: A  109 THR cc_start: 0.8772 (m) cc_final: 0.8518 (p)
REVERT: A  118 VAL cc_start: 0.9571 (m) cc_final: 0.9281 (p)
REVERT: A  154 MET cc_start: 0.8721 (tpt) cc_final: 0.8372 (tpt)
REVERT: A  245 ASP cc_start: 0.7908 (p0) cc_final: 0.7476 (p0)
REVERT: A  267 PHE cc_start: 0.9024 (m-80) cc_final: 0.8641 (m-10)
REVERT: A  302 MET cc_start: 0.9479 (mmp) cc_final: 0.8851 (mpp)
REVERT: H  290 GLU cc_start: 0.7892 (tp30) cc_final: 0.7592 (tp30)
REVERT: H  309 HIS cc_start: 0.9224 (m-70) cc_final: 0.9010 (m-70)
REVERT: H  413 MET cc_start: 0.7863 (mmt) cc_final: 0.6973 (mmt)
REVERT: K  144 PHE cc_start: 0.9041 (t80) cc_final: 0.8400 (t80)
REVERT: K  153 CYS cc_start: 0.8954 (t) cc_final: 0.8616 (m)
REVERT: K  190 MET cc_start: 0.9348 (tmm) cc_final: 0.9053 (tmm)
REVERT: K  215 HIS cc_start: 0.9288 (m-70) cc_final: 0.8468 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0912
  time to fit residues: 14.9727
Evaluate side-chains
  93 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 12 optimal weight:    0.2980
   chunk 84 optimal weight:   30.0000
   chunk 98 optimal weight:   30.0000
   chunk 29 optimal weight:   20.0000
   chunk 11 optimal weight:    0.6980
   chunk 74 optimal weight:    5.9990
   chunk 34 optimal weight:    7.9990
   chunk 95 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   chunk 61 optimal weight:   20.0000
   chunk 23 optimal weight:    3.9990
   overall best weight:    3.5986

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

Flipped N/Q/H residues before XYZ refinement:
A  61 HIS
** H   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 433 GLN ** 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 = 0.3592 r_free = 0.3592 target = 0.067059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.046968 restraints weight = 70860.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.049138 restraints weight = 35193.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.050543 restraints weight = 22229.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.051457 restraints weight = 16407.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.052045 restraints weight = 13474.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.7164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9671  Z= 0.121
  Angle     :  0.471   6.854  13103  Z= 0.252
  Chirality :  0.039   0.141   1454
  Planarity :  0.012   0.464   1703
  Dihedral  : 10.169 169.670   1350
  Min Nonbonded Distance : 1.837

Molprobity Statistics.
  All-atom Clashscore : 46.54
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.35 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.25), residues: 1193
  helix:  2.02 (0.23), residues: 526
  sheet: -0.70 (0.37), residues: 188
  loop : -0.47 (0.30), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG K 297 
 TYR   0.013   0.001   TYR K   4 
 PHE   0.022   0.001   PHE K 293 
 TRP   0.012   0.001   TRP H  21 
 HIS   0.003   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 9667)
  covalent geometry    : angle       0.47081 (13103)
  hydrogen bonds       : bond        0.03439 (  481)
  hydrogen bonds       : angle       4.66246 ( 1461)
  Misc. bond           : bond        0.00321 (    4)

===============================================================================
Job complete
usr+sys time: 1556.78 seconds
wall clock time: 27 minutes 48.86 seconds (1668.86 seconds total)