Starting phenix.real_space_refine
on Sun Jan 19 09:00:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8va2_43085/01_2025/8va2_43085.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8va2_43085/01_2025/8va2_43085.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8va2_43085/01_2025/8va2_43085.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8va2_43085/01_2025/8va2_43085.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8va2_43085/01_2025/8va2_43085.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8va2_43085/01_2025/8va2_43085.cif"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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: 6
    Type Number    sf(0)   Gaussians
     P      10      5.49       5
     Mg      2      5.21       5
     S      74      5.16       5
     C    8470      2.51       5
     N    2304      2.21       5
     O    2570      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 13430
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "a"
      Number of atoms: 3290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 419, 3290
          Classifications: {'peptide': 419}
          Link IDs: {'PTRANS': 20, 'TRANS': 398}
          Chain breaks: 2
    Chain: "b"
      Number of atoms: 3290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 419, 3290
          Classifications: {'peptide': 419}
          Link IDs: {'PTRANS': 20, 'TRANS': 398}
          Chain breaks: 2
    Chain: "g"
      Number of atoms: 3323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 414, 3323
          Classifications: {'peptide': 414}
          Link IDs: {'PTRANS': 20, 'TRANS': 393}
          Chain breaks: 4
    Chain: "h"
      Number of atoms: 3405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 425, 3405
          Classifications: {'peptide': 425}
          Link IDs: {'PTRANS': 20, 'TRANS': 404}
          Chain breaks: 3
    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: "b"
      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: "g"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "h"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.91, per 1000 atoms: 0.59
  Number of scatterers: 13430
  At special positions: 0
  Unit cell: (113.52, 110.88, 125.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      74     16.00
     P      10     15.00
     Mg      2     11.99
     O    2570      8.00
     N    2304      7.00
     C    8470      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.65
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3154

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 13 sheets defined
      53.5% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.38
  Creating SS restraints...
    Processing helix  chain 'a' and resid 10 through 28
    Processing helix  chain 'a' and resid 47 through 51
      removed outlier: 3.841A  pdb=" N   THR a  51 " --> pdb=" O   SER a  48 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 72 through 80
    Processing helix  chain 'a' and resid 110 through 113
    Processing helix  chain 'a' and resid 114 through 129
      removed outlier: 3.711A  pdb=" N   GLN a 128 " --> pdb=" O   LYS a 124 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   CYS a 129 " --> pdb=" O   LEU a 125 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 143 through 161
    Processing helix  chain 'a' and resid 182 through 198
      removed outlier: 3.683A  pdb=" N   HIS a 197 " --> pdb=" O   THR a 193 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 205 through 216
    Processing helix  chain 'a' and resid 223 through 244
      removed outlier: 3.972A  pdb=" N   SER a 241 " --> pdb=" O   SER a 237 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 251 through 260
      removed outlier: 3.532A  pdb=" N   VAL a 260 " --> pdb=" O   GLN a 256 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 278 through 283
      removed outlier: 3.866A  pdb=" N   TYR a 282 " --> pdb=" O   GLU a 279 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 287 through 297
    Processing helix  chain 'a' and resid 298 through 301
    Processing helix  chain 'a' and resid 324 through 338
      removed outlier: 3.575A  pdb=" N   LYS a 338 " --> pdb=" O   THR a 334 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 382 through 402
      removed outlier: 3.827A  pdb=" N   GLU a 386 " --> pdb=" O   THR a 382 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   LYS a 401 " --> pdb=" O   LEU a 397 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ARG a 402 " --> pdb=" O   MET a 398 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 405 through 410
    Processing helix  chain 'a' and resid 414 through 436
      removed outlier: 3.562A  pdb=" N   PHE a 418 " --> pdb=" O   GLU a 414 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 9 through 29
    Processing helix  chain 'b' and resid 48 through 51
    Processing helix  chain 'b' and resid 71 through 81
      removed outlier: 4.762A  pdb=" N   ILE b  75 " --> pdb=" O   GLU b  71 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 103 through 108
    Processing helix  chain 'b' and resid 110 through 129
      removed outlier: 3.821A  pdb=" N   ILE b 114 " --> pdb=" O   ILE b 110 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   ASP b 116 " --> pdb=" O   LYS b 112 " (cutoff:3.500A)
      removed outlier: 5.403A  pdb=" N   LEU b 117 " --> pdb=" O   GLU b 113 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLN b 128 " --> pdb=" O   LYS b 124 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 143 through 161
    Processing helix  chain 'b' and resid 182 through 195
    Processing helix  chain 'b' and resid 205 through 216
      removed outlier: 3.580A  pdb=" N   ILE b 209 " --> pdb=" O   ASP b 205 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 223 through 244
      removed outlier: 4.377A  pdb=" N   SER b 241 " --> pdb=" O   SER b 237 " (cutoff:3.500A)
      removed outlier: 4.969A  pdb=" N   LEU b 242 " --> pdb=" O   ILE b 238 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 251 through 259
      removed outlier: 3.625A  pdb=" N   LEU b 259 " --> pdb=" O   PHE b 255 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 277 through 282
      removed outlier: 4.014A  pdb=" N   TYR b 282 " --> pdb=" O   ALA b 278 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 287 through 297
    Processing helix  chain 'b' and resid 324 through 338
      removed outlier: 3.768A  pdb=" N   LYS b 338 " --> pdb=" O   THR b 334 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 382 through 402
      removed outlier: 3.661A  pdb=" N   GLU b 386 " --> pdb=" O   THR b 382 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LYS b 401 " --> pdb=" O   LEU b 397 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 405 through 410
      removed outlier: 4.254A  pdb=" N   GLY b 410 " --> pdb=" O   HIS b 406 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 414 through 437
    Processing helix  chain 'g' and resid 10 through 29
    Processing helix  chain 'g' and resid 71 through 78
    Processing helix  chain 'g' and resid 82 through 86
    Processing helix  chain 'g' and resid 103 through 114
    Processing helix  chain 'g' and resid 114 through 128
      removed outlier: 3.588A  pdb=" N   ILE g 118 " --> pdb=" O   ILE g 114 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLY g 128 " --> pdb=" O   ARG g 124 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 143 through 159
    Processing helix  chain 'g' and resid 183 through 198
      removed outlier: 3.640A  pdb=" N   ASN g 187 " --> pdb=" O   VAL g 183 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 206 through 217
    Processing helix  chain 'g' and resid 224 through 245
      removed outlier: 4.998A  pdb=" N   THR g 242 " --> pdb=" O   ALA g 238 " (cutoff:3.500A)
      removed outlier: 5.393A  pdb=" N   LEU g 243 " --> pdb=" O   SER g 239 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 252 through 259
    Processing helix  chain 'g' and resid 289 through 297
      removed outlier: 3.517A  pdb=" N   MET g 294 " --> pdb=" O   VAL g 290 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 329 through 344
    Processing helix  chain 'g' and resid 384 through 400
      removed outlier: 3.732A  pdb=" N   PHE g 388 " --> pdb=" O   ILE g 384 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 407 through 411
    Processing helix  chain 'g' and resid 418 through 439
    Processing helix  chain 'h' and resid 11 through 29
    Processing helix  chain 'h' and resid 39 through 44
      removed outlier: 3.879A  pdb=" N   GLU h  43 " --> pdb=" O   PHE h  40 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 47 through 51
      removed outlier: 3.602A  pdb=" N   VAL h  50 " --> pdb=" O   ARG h  47 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   PHE h  51 " --> pdb=" O   LYS h  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'h' and resid 47 through 51'
    Processing helix  chain 'h' and resid 70 through 79
      removed outlier: 4.667A  pdb=" N   ILE h  74 " --> pdb=" O   GLU h  70 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 82 through 86
    Processing helix  chain 'h' and resid 87 through 91
    Processing helix  chain 'h' and resid 103 through 129
      removed outlier: 5.832A  pdb=" N   GLU h 116 " --> pdb=" O   GLU h 112 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   ASP h 117 " --> pdb=" O   LYS h 113 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   GLY h 128 " --> pdb=" O   ARG h 124 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   SER h 129 " --> pdb=" O   GLU h 125 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 143 through 161
    Processing helix  chain 'h' and resid 183 through 199
      removed outlier: 3.517A  pdb=" N   ASN h 187 " --> pdb=" O   VAL h 183 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 207 through 219
      removed outlier: 3.571A  pdb=" N   HIS h 219 " --> pdb=" O   THR h 215 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 223 through 245
      removed outlier: 3.642A  pdb=" N   GLN h 227 " --> pdb=" O   PRO h 223 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 252 through 259
    Processing helix  chain 'h' and resid 263 through 267
    Processing helix  chain 'h' and resid 280 through 285
      removed outlier: 3.693A  pdb=" N   VAL h 285 " --> pdb=" O   SER h 281 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 289 through 299
      removed outlier: 3.699A  pdb=" N   GLN h 299 " --> pdb=" O   ARG h 295 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 300 through 303
    Processing helix  chain 'h' and resid 329 through 344
    Processing helix  chain 'h' and resid 384 through 402
      removed outlier: 4.081A  pdb=" N   PHE h 388 " --> pdb=" O   ILE h 384 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ARG h 401 " --> pdb=" O   LYS h 397 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 405 through 410
    Processing helix  chain 'h' and resid 411 through 416
      removed outlier: 4.264A  pdb=" N   ASP h 416 " --> pdb=" O   ASP h 412 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 418 through 440
      removed outlier: 4.094A  pdb=" N   THR h 439 " --> pdb=" O   TYR h 435 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   ARG h 440 " --> pdb=" O   HIS h 436 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'a' and resid 65 through 68
      removed outlier: 3.737A  pdb=" N   ILE a   5 " --> pdb=" O   GLY a 134 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'a' and resid 53 through 55
      removed outlier: 3.696A  pdb=" N   SER a  54 " --> pdb=" O   VAL a  62 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'a' and resid 353 through 356
    Processing sheet with id=AA4, first strand: chain 'b' and resid 65 through 66
      removed outlier: 3.522A  pdb=" N   VAL b  66 " --> pdb=" O   SER b   6 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ILE b   5 " --> pdb=" O   GLY b 134 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   CYS b 200 " --> pdb=" O   LYS b 166 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'b' and resid 53 through 55
    Processing sheet with id=AA6, first strand: chain 'b' and resid 269 through 270
      removed outlier: 3.629A  pdb=" N   SER b 379 " --> pdb=" O   LEU b 269 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'b' and resid 320 through 321
    Processing sheet with id=AA8, first strand: chain 'g' and resid 64 through 66
      removed outlier: 8.647A  pdb=" N   VAL g  65 " --> pdb=" O   ILE g   5 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   THR g   7 " --> pdb=" O   VAL g  65 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ILE g   6 " --> pdb=" O   GLY g 134 " (cutoff:3.500A)
      removed outlier: 5.885A  pdb=" N   PHE g 135 " --> pdb=" O   GLN g 167 " (cutoff:3.500A)
      removed outlier: 7.701A  pdb=" N   TYR g 169 " --> pdb=" O   PHE g 135 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   LEU g 137 " --> pdb=" O   TYR g 169 " (cutoff:3.500A)
      removed outlier: 7.729A  pdb=" N   VAL g 171 " --> pdb=" O   LEU g 137 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   HIS g 139 " --> pdb=" O   VAL g 171 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   VAL g 166 " --> pdb=" O   CYS g 201 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'g' and resid 52 through 54
      removed outlier: 3.517A  pdb=" N   TYR g  53 " --> pdb=" O   ILE g  61 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'g' and resid 270 through 273
      removed outlier: 6.575A  pdb=" N   ASN g 380 " --> pdb=" O   ILE g 318 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'g' and resid 270 through 273
      removed outlier: 4.000A  pdb=" N   LEU g 321 " --> pdb=" O   MET g 378 " (cutoff:3.500A)
      removed outlier: 5.681A  pdb=" N   ASN g 322 " --> pdb=" O   ALA g 359 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'h' and resid 66 through 67
      removed outlier: 7.866A  pdb=" N   LEU h  67 " --> pdb=" O   THR h   7 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   GLN h   9 " --> pdb=" O   LEU h  67 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ILE h   6 " --> pdb=" O   GLY h 134 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU h  10 " --> pdb=" O   CYS h 138 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   PHE h 135 " --> pdb=" O   GLN h 167 " (cutoff:3.500A)
      removed outlier: 7.938A  pdb=" N   TYR h 169 " --> pdb=" O   PHE h 135 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   LEU h 137 " --> pdb=" O   TYR h 169 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   VAL h 171 " --> pdb=" O   LEU h 137 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'h' and resid 357 through 361
      removed outlier: 9.206A  pdb=" N   GLN h 357 " --> pdb=" O   ILE h 318 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ILE h 320 " --> pdb=" O   GLN h 357 " (cutoff:3.500A)
      removed outlier: 8.408A  pdb=" N   ALA h 359 " --> pdb=" O   ILE h 320 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   ASN h 322 " --> pdb=" O   ALA h 359 " (cutoff:3.500A)
      removed outlier: 7.575A  pdb=" N   SER h 361 " --> pdb=" O   ASN h 322 " (cutoff:3.500A)
      removed outlier: 5.856A  pdb=" N   ILE h 324 " --> pdb=" O   SER h 361 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ALA h 319 " --> pdb=" O   ASN h 380 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   SER h 374 " --> pdb=" O   GLN h 325 " (cutoff:3.500A)

    651 hydrogen bonds defined for protein.
    1875 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: 3.74

  Time building geometry restraints manager: 4.13 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4440
        1.34 -     1.47: 3191
        1.47 -     1.59: 5970
        1.59 -     1.71: 4
        1.71 -     1.83: 118
  Bond restraints: 13723
  Sorted by residual:
  bond pdb=" O5' GTP b 501 "
       pdb=" PA  GTP b 501 "
    ideal  model  delta    sigma   weight residual
    1.610  1.831 -0.221 2.00e-02 2.50e+03 1.22e+02
  bond pdb=" O5' GTP a 501 "
       pdb=" PA  GTP a 501 "
    ideal  model  delta    sigma   weight residual
    1.610  1.828 -0.218 2.00e-02 2.50e+03 1.19e+02
  bond pdb=" O5' GDP h 501 "
       pdb=" PA  GDP h 501 "
    ideal  model  delta    sigma   weight residual
    1.610  1.745 -0.135 2.00e-02 2.50e+03 4.56e+01
  bond pdb=" O5' GDP g 501 "
       pdb=" PA  GDP g 501 "
    ideal  model  delta    sigma   weight residual
    1.610  1.731 -0.121 2.00e-02 2.50e+03 3.64e+01
  bond pdb=" O3A GDP h 501 "
       pdb=" PB  GDP h 501 "
    ideal  model  delta    sigma   weight residual
    1.610  1.730 -0.120 2.00e-02 2.50e+03 3.62e+01
  ... (remaining 13718 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.03: 18530
        4.03 -     8.06: 63
        8.06 -    12.09: 27
       12.09 -    16.12: 19
       16.12 -    20.15: 3
  Bond angle restraints: 18642
  Sorted by residual:
  angle pdb=" PA  GDP g 501 "
        pdb=" O3A GDP g 501 "
        pdb=" PB  GDP g 501 "
      ideal   model   delta    sigma   weight residual
     120.50  140.65  -20.15 3.00e+00 1.11e-01 4.51e+01
  angle pdb=" PA  GDP h 501 "
        pdb=" O3A GDP h 501 "
        pdb=" PB  GDP h 501 "
      ideal   model   delta    sigma   weight residual
     120.50  140.38  -19.88 3.00e+00 1.11e-01 4.39e+01
  angle pdb=" O2B GTP b 501 "
        pdb=" PB  GTP b 501 "
        pdb=" O3A GTP b 501 "
      ideal   model   delta    sigma   weight residual
     109.50   92.63   16.87 3.00e+00 1.11e-01 3.16e+01
  angle pdb=" O2B GTP a 501 "
        pdb=" PB  GTP a 501 "
        pdb=" O3A GTP a 501 "
      ideal   model   delta    sigma   weight residual
     109.50   93.99   15.51 3.00e+00 1.11e-01 2.67e+01
  angle pdb=" O1A GTP a 501 "
        pdb=" PA  GTP a 501 "
        pdb=" O5' GTP a 501 "
      ideal   model   delta    sigma   weight residual
     108.20   93.51   14.69 3.00e+00 1.11e-01 2.40e+01
  ... (remaining 18637 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.50: 8007
       33.50 -    66.99: 178
       66.99 -   100.49: 17
      100.49 -   133.99: 5
      133.99 -   167.48: 5
  Dihedral angle restraints: 8212
    sinusoidal: 3328
      harmonic: 4884
  Sorted by residual:
  dihedral pdb=" C8  GTP b 501 "
           pdb=" C1' GTP b 501 "
           pdb=" N9  GTP b 501 "
           pdb=" O4' GTP b 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -62.89  167.48     1      2.00e+01 2.50e-03 4.74e+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  -60.69  165.28     1      2.00e+01 2.50e-03 4.72e+01
  dihedral pdb=" O5' GTP a 501 "
           pdb=" O3A GTP a 501 "
           pdb=" PA  GTP a 501 "
           pdb=" PB  GTP a 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     274.12  110.56  163.57     1      2.00e+01 2.50e-03 4.70e+01
  ... (remaining 8209 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 1888
       0.075 -    0.149: 179
       0.149 -    0.224: 2
       0.224 -    0.298: 5
       0.298 -    0.373: 5
  Chirality restraints: 2079
  Sorted by residual:
  chirality pdb=" C2' GDP h 501 "
            pdb=" C3' GDP h 501 "
            pdb=" O2' GDP h 501 "
            pdb=" C1' GDP h 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.88    0.37 2.00e-01 2.50e+01 3.47e+00
  chirality pdb=" C3' GTP b 501 "
            pdb=" C2' GTP b 501 "
            pdb=" C4' GTP b 501 "
            pdb=" O3' GTP b 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.84    0.37 2.00e-01 2.50e+01 3.40e+00
  chirality pdb=" C3' GTP a 501 "
            pdb=" C2' GTP a 501 "
            pdb=" C4' GTP a 501 "
            pdb=" O3' GTP a 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.82    0.35 2.00e-01 2.50e+01 3.02e+00
  ... (remaining 2076 not shown)

  Planarity restraints: 2403
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL b 324 "   -0.028 5.00e-02 4.00e+02   4.20e-02 2.82e+00
        pdb=" N   PRO b 325 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO b 325 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO b 325 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN g  16 "   -0.008 2.00e-02 2.50e+03   1.58e-02 2.50e+00
        pdb=" C   GLN g  16 "    0.027 2.00e-02 2.50e+03
        pdb=" O   GLN g  16 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ILE g  17 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG b 229 "   -0.118 9.50e-02 1.11e+02   5.35e-02 2.24e+00
        pdb=" NE  ARG b 229 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG b 229 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG b 229 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG b 229 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 2400 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.47: 166
        2.47 -     3.08: 11301
        3.08 -     3.69: 21644
        3.69 -     4.29: 30287
        4.29 -     4.90: 49037
  Nonbonded interactions: 112435
  Sorted by model distance:
  nonbonded pdb=" O2G GTP a 501 "
            pdb="MG    MG a 502 "
     model   vdw
     1.868 2.170
  nonbonded pdb=" O2B GTP a 501 "
            pdb="MG    MG a 502 "
     model   vdw
     1.888 2.170
  nonbonded pdb=" O2G GTP b 501 "
            pdb="MG    MG b 502 "
     model   vdw
     1.890 2.170
  nonbonded pdb=" O   HIS g 436 "
            pdb=" OG1 THR g 439 "
     model   vdw
     2.043 3.040
  nonbonded pdb=" O   ARG a 214 "
            pdb=" NH1 ARG a 214 "
     model   vdw
     2.122 3.120
  ... (remaining 112430 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'a'
  selection = chain 'b'
}
ncs_group {
  reference = chain 'g'
  selection = (chain 'h' and (resid 4 through 278 or resid 290 through 441 or resid 501))
}

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:             2.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.530
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     30.700
  Find NCS groups from input model:        0.580
  Set up NCS constraints:                  0.060
  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:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
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      :  0.006   0.221  13723  Z= 0.415
  Angle     :  0.873  20.146  18642  Z= 0.360
  Chirality :  0.046   0.373   2079
  Planarity :  0.003   0.053   2403
  Dihedral  : 15.735 167.483   5058
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.21), residues: 1647
  helix:  1.20 (0.19), residues: 755
  sheet: -1.82 (0.36), residues: 209
  loop : -1.31 (0.25), residues: 683

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP g 351 
 HIS   0.006   0.001   HIS a  28 
 PHE   0.016   0.001   PHE g 119 
 TYR   0.016   0.001   TYR b 399 
 ARG   0.012   0.000   ARG b 229 

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

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

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 309
  time to evaluate  : 2.110 
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: a  203 MET cc_start: 0.8895 (mmp) cc_final: 0.7801 (mmp)
REVERT: a  259 LEU cc_start: 0.9375 (mt) cc_final: 0.9155 (mt)
REVERT: a  377 MET cc_start: 0.8759 (ttp) cc_final: 0.8540 (ttp)
REVERT: b  152 LEU cc_start: 0.9639 (tp) cc_final: 0.9351 (tp)
REVERT: b  176 GLN cc_start: 0.8675 (mm110) cc_final: 0.8466 (mm-40)
REVERT: b  183 GLU cc_start: 0.8533 (mp0) cc_final: 0.8207 (mp0)
REVERT: b  185 TYR cc_start: 0.7832 (m-10) cc_final: 0.7221 (m-10)
REVERT: b  203 MET cc_start: 0.9493 (mmp) cc_final: 0.8607 (mmm)
REVERT: b  217 LEU cc_start: 0.8593 (mt) cc_final: 0.8265 (mt)
REVERT: b  313 MET cc_start: 0.7661 (mtt) cc_final: 0.7209 (mpp)
REVERT: b  318 LEU cc_start: 0.9098 (mt) cc_final: 0.8718 (mt)
REVERT: g  244 ARG cc_start: 0.9033 (mtm-85) cc_final: 0.8568 (mpp80)
REVERT: g  270 MET cc_start: 0.8283 (ptp) cc_final: 0.7831 (pmm)
REVERT: g  378 MET cc_start: 0.8896 (mpp) cc_final: 0.8653 (mpp)
REVERT: g  388 PHE cc_start: 0.8925 (m-10) cc_final: 0.8649 (m-10)
REVERT: g  397 LYS cc_start: 0.8700 (tttt) cc_final: 0.7995 (mmmt)
REVERT: g  421 MET cc_start: 0.9023 (mtp) cc_final: 0.8722 (mtp)
REVERT: h   15 ASN cc_start: 0.8452 (m110) cc_final: 0.8163 (m110)
REVERT: h   20 GLU cc_start: 0.8352 (tp30) cc_final: 0.7989 (tp30)
REVERT: h  154 LEU cc_start: 0.9075 (mt) cc_final: 0.8829 (mt)
REVERT: h  270 MET cc_start: 0.7221 (ttt) cc_final: 0.6996 (ttt)
REVERT: h  271 THR cc_start: 0.7637 (p) cc_final: 0.7194 (p)
REVERT: h  321 LEU cc_start: 0.9117 (tp) cc_final: 0.8820 (tp)
REVERT: h  429 GLN cc_start: 0.8845 (mt0) cc_final: 0.8608 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 309
  average time/residue: 0.2449
  time to fit residues: 113.0237
Evaluate side-chains
  250 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 250
  time to evaluate  : 1.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 139 optimal weight:    0.9980
   chunk 125 optimal weight:    0.2980
   chunk 69 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 129 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 96 optimal weight:    0.6980
   chunk 149 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
a 186 ASN
a 233 GLN
a 258 ASN
** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** g 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
h 230 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.076746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.067465 restraints weight = 53383.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.069423 restraints weight = 31944.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.070900 restraints weight = 21160.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.094  13723  Z= 0.252
  Angle     :  0.626   7.213  18642  Z= 0.320
  Chirality :  0.046   0.215   2079
  Planarity :  0.004   0.053   2403
  Dihedral  : 10.920 179.856   1871
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  6.62 %
    Favored  : 93.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.21), residues: 1647
  helix:  1.18 (0.19), residues: 764
  sheet: -1.84 (0.32), residues: 242
  loop : -1.01 (0.25), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP a 388 
 HIS   0.011   0.001   HIS h  29 
 PHE   0.021   0.002   PHE h  21 
 TYR   0.016   0.001   TYR g 395 
 ARG   0.005   0.001   ARG a 214 

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

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

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 319
  time to evaluate  : 1.552 
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: a  167 LEU cc_start: 0.9183 (mm) cc_final: 0.8872 (mm)
REVERT: a  203 MET cc_start: 0.8974 (mmp) cc_final: 0.7776 (mmp)
REVERT: a  254 ASP cc_start: 0.7621 (t70) cc_final: 0.7054 (t70)
REVERT: a  337 THR cc_start: 0.8457 (p) cc_final: 0.8237 (p)
REVERT: a  349 THR cc_start: 0.9250 (p) cc_final: 0.9032 (p)
REVERT: b  185 TYR cc_start: 0.7780 (m-10) cc_final: 0.7334 (m-10)
REVERT: b  203 MET cc_start: 0.9446 (mmp) cc_final: 0.8443 (mmm)
REVERT: b  217 LEU cc_start: 0.8614 (mt) cc_final: 0.8276 (mt)
REVERT: b  260 VAL cc_start: 0.8916 (t) cc_final: 0.8597 (m)
REVERT: b  313 MET cc_start: 0.7525 (mtt) cc_final: 0.7215 (mpp)
REVERT: b  377 MET cc_start: 0.8692 (tmm) cc_final: 0.8206 (tmm)
REVERT: g   22 TRP cc_start: 0.8540 (m100) cc_final: 0.8227 (m100)
REVERT: g   52 PHE cc_start: 0.8623 (m-80) cc_final: 0.8374 (m-80)
REVERT: g  197 GLN cc_start: 0.9315 (mm-40) cc_final: 0.9067 (mm-40)
REVERT: g  377 MET cc_start: 0.8424 (tmm) cc_final: 0.8057 (tmm)
REVERT: g  392 CYS cc_start: 0.8510 (p) cc_final: 0.8257 (p)
REVERT: g  397 LYS cc_start: 0.8753 (tttt) cc_final: 0.8328 (mmmt)
REVERT: h   15 ASN cc_start: 0.8467 (m110) cc_final: 0.8045 (m110)
REVERT: h   20 GLU cc_start: 0.8405 (tp30) cc_final: 0.8078 (tp30)
REVERT: h  204 VAL cc_start: 0.9300 (t) cc_final: 0.9006 (t)
REVERT: h  271 THR cc_start: 0.7862 (p) cc_final: 0.7352 (p)
  outliers start: 4
  outliers final: 0
  residues processed: 321
  average time/residue: 0.2275
  time to fit residues: 111.3907
Evaluate side-chains
  243 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 1.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 163 optimal weight:    0.9990
   chunk 115 optimal weight:    2.9990
   chunk 148 optimal weight:    2.9990
   chunk 118 optimal weight:    0.4980
   chunk 140 optimal weight:    0.0370
   chunk 74 optimal weight:    2.9990
   chunk 34 optimal weight:    0.1980
   chunk 81 optimal weight:    0.9990
   chunk 133 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.4860

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

Flipped N/Q/H residues before XYZ refinement:
a  11 GLN
** a 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
a 186 ASN
a 233 GLN
** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 309 HIS
** g  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
g 158 ASN
** g 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
h 167 GLN
h 187 ASN
h 302 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.077669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.068293 restraints weight = 52898.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.070270 restraints weight = 31332.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.071782 restraints weight = 20837.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  13723  Z= 0.208
  Angle     :  0.601   6.696  18642  Z= 0.306
  Chirality :  0.045   0.230   2079
  Planarity :  0.004   0.052   2403
  Dihedral  : 10.062 167.179   1871
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  4.37 %
    Favored  : 95.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.21), residues: 1647
  helix:  1.21 (0.18), residues: 763
  sheet: -1.67 (0.32), residues: 236
  loop : -0.90 (0.25), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP a  21 
 HIS   0.006   0.001   HIS g 115 
 PHE   0.018   0.001   PHE g 225 
 TYR   0.016   0.001   TYR b 172 
 ARG   0.004   0.000   ARG g 244 

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

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

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 321
  time to evaluate  : 1.540 
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  167 LEU cc_start: 0.9216 (mm) cc_final: 0.8882 (mm)
REVERT: a  196 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6863 (mm-30)
REVERT: a  203 MET cc_start: 0.8977 (mmp) cc_final: 0.7785 (mmp)
REVERT: a  377 MET cc_start: 0.8666 (ttp) cc_final: 0.8398 (ttp)
REVERT: b  152 LEU cc_start: 0.9723 (tp) cc_final: 0.9460 (tp)
REVERT: b  157 LEU cc_start: 0.8898 (mp) cc_final: 0.8696 (mt)
REVERT: b  185 TYR cc_start: 0.7729 (m-10) cc_final: 0.7279 (m-10)
REVERT: b  203 MET cc_start: 0.9375 (mmp) cc_final: 0.8526 (mmm)
REVERT: b  210 TYR cc_start: 0.8438 (m-80) cc_final: 0.7939 (m-80)
REVERT: b  217 LEU cc_start: 0.8647 (mt) cc_final: 0.8337 (mt)
REVERT: b  260 VAL cc_start: 0.8950 (t) cc_final: 0.8533 (p)
REVERT: g   52 PHE cc_start: 0.8614 (m-80) cc_final: 0.8335 (m-80)
REVERT: g  197 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8925 (mm-40)
REVERT: g  198 ASN cc_start: 0.8014 (m-40) cc_final: 0.7450 (m-40)
REVERT: g  253 LEU cc_start: 0.8728 (tp) cc_final: 0.8223 (tp)
REVERT: g  335 LYS cc_start: 0.9369 (mmpt) cc_final: 0.9078 (mmmt)
REVERT: g  392 CYS cc_start: 0.8482 (p) cc_final: 0.8229 (p)
REVERT: g  397 LYS cc_start: 0.8571 (tttt) cc_final: 0.8180 (mmmt)
REVERT: g  421 MET cc_start: 0.9013 (mtp) cc_final: 0.8718 (mtp)
REVERT: h   15 ASN cc_start: 0.8599 (m110) cc_final: 0.8219 (m110)
REVERT: h   20 GLU cc_start: 0.8504 (tp30) cc_final: 0.8150 (tp30)
REVERT: h  271 THR cc_start: 0.7864 (p) cc_final: 0.7343 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 321
  average time/residue: 0.2329
  time to fit residues: 111.7409
Evaluate side-chains
  255 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 1.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 143 optimal weight:    0.0970
   chunk 118 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9980
   chunk 95 optimal weight:    0.8980
   chunk 123 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9980
   chunk 137 optimal weight:    0.9980
   chunk 125 optimal weight:    0.5980
   chunk 159 optimal weight:    2.9990
   chunk 122 optimal weight:    0.8980
   chunk 111 optimal weight:    1.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
a  11 GLN
a 186 ASN
a 233 GLN
a 301 GLN
** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
g  15 ASN
** g 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
g 158 ASN
** h  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
h 302 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.077578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.068277 restraints weight = 52432.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.070317 restraints weight = 31230.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.071794 restraints weight = 20640.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080  13723  Z= 0.222
  Angle     :  0.596   6.871  18642  Z= 0.303
  Chirality :  0.045   0.237   2079
  Planarity :  0.004   0.050   2403
  Dihedral  :  9.712 157.418   1871
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  4.98 %
    Favored  : 94.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.21), residues: 1647
  helix:  1.20 (0.18), residues: 765
  sheet: -1.57 (0.32), residues: 239
  loop : -0.78 (0.25), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP b 346 
 HIS   0.007   0.001   HIS h 334 
 PHE   0.021   0.002   PHE h  21 
 TYR   0.024   0.001   TYR g 169 
 ARG   0.008   0.000   ARG b 422 

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

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

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 326
  time to evaluate  : 1.641 
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: a   69 ASP cc_start: 0.6730 (m-30) cc_final: 0.6437 (m-30)
REVERT: a  167 LEU cc_start: 0.9155 (mm) cc_final: 0.8924 (mm)
REVERT: a  196 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6833 (mm-30)
REVERT: a  203 MET cc_start: 0.8979 (mmp) cc_final: 0.7877 (mmp)
REVERT: a  293 ASN cc_start: 0.9142 (t0) cc_final: 0.8876 (t0)
REVERT: b   77 GLU cc_start: 0.8980 (pp20) cc_final: 0.8770 (pp20)
REVERT: b  152 LEU cc_start: 0.9729 (tp) cc_final: 0.9431 (tp)
REVERT: b  185 TYR cc_start: 0.7620 (m-10) cc_final: 0.7257 (m-10)
REVERT: b  187 SER cc_start: 0.9139 (m) cc_final: 0.8859 (p)
REVERT: b  210 TYR cc_start: 0.8490 (m-80) cc_final: 0.8057 (m-80)
REVERT: b  217 LEU cc_start: 0.8536 (mt) cc_final: 0.8266 (mt)
REVERT: b  260 VAL cc_start: 0.8977 (t) cc_final: 0.8547 (p)
REVERT: b  290 GLU cc_start: 0.8832 (pt0) cc_final: 0.8614 (pt0)
REVERT: b  313 MET cc_start: 0.7805 (mpp) cc_final: 0.7576 (mpp)
REVERT: g   15 ASN cc_start: 0.9140 (m110) cc_final: 0.8810 (m110)
REVERT: g   22 TRP cc_start: 0.8500 (m100) cc_final: 0.8089 (m100)
REVERT: g  103 ASN cc_start: 0.7559 (m110) cc_final: 0.7212 (m110)
REVERT: g  135 PHE cc_start: 0.9123 (m-10) cc_final: 0.8914 (m-10)
REVERT: g  197 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8923 (mm-40)
REVERT: g  198 ASN cc_start: 0.7581 (m-40) cc_final: 0.7076 (m-40)
REVERT: g  335 LYS cc_start: 0.9412 (mmpt) cc_final: 0.9154 (mmmt)
REVERT: g  377 MET cc_start: 0.8307 (tmm) cc_final: 0.7862 (tmm)
REVERT: g  392 CYS cc_start: 0.8342 (p) cc_final: 0.8140 (p)
REVERT: g  397 LYS cc_start: 0.8585 (tttt) cc_final: 0.8222 (mmmt)
REVERT: g  421 MET cc_start: 0.9011 (mtp) cc_final: 0.8708 (mtp)
REVERT: h   15 ASN cc_start: 0.8601 (m110) cc_final: 0.8230 (m110)
REVERT: h   20 GLU cc_start: 0.8424 (tp30) cc_final: 0.7976 (tp30)
REVERT: h  154 LEU cc_start: 0.9097 (mt) cc_final: 0.8885 (mt)
REVERT: h  155 GLU cc_start: 0.9187 (tt0) cc_final: 0.8652 (pt0)
REVERT: h  271 THR cc_start: 0.7530 (p) cc_final: 0.7267 (p)
REVERT: h  292 ASP cc_start: 0.9137 (p0) cc_final: 0.8924 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 326
  average time/residue: 0.2404
  time to fit residues: 117.4361
Evaluate side-chains
  251 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 1.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0470
   chunk 2 optimal weight:    1.9990
   chunk 162 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 125 optimal weight:    1.9990
   chunk 149 optimal weight:    0.6980
   chunk 73 optimal weight:    0.0870
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
a  11 GLN
a  61 HIS
a 186 ASN
a 233 GLN
a 301 GLN
** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
g 175 GLN
** h  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
h 167 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.078398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.069104 restraints weight = 52871.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.071117 restraints weight = 31375.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.072572 restraints weight = 20855.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  13723  Z= 0.197
  Angle     :  0.603   7.281  18642  Z= 0.306
  Chirality :  0.045   0.199   2079
  Planarity :  0.004   0.046   2403
  Dihedral  :  9.515 156.395   1871
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.21), residues: 1647
  helix:  1.19 (0.19), residues: 770
  sheet: -1.21 (0.35), residues: 220
  loop : -0.75 (0.24), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP a 388 
 HIS   0.007   0.001   HIS g 115 
 PHE   0.020   0.001   PHE a 351 
 TYR   0.021   0.001   TYR g 169 
 ARG   0.005   0.000   ARG b 308 

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

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

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 318
  time to evaluate  : 1.649 
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   69 ASP cc_start: 0.6816 (m-30) cc_final: 0.6367 (m-30)
REVERT: a  167 LEU cc_start: 0.9116 (mm) cc_final: 0.8727 (mm)
REVERT: a  196 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6963 (mm-30)
REVERT: b   77 GLU cc_start: 0.8922 (pp20) cc_final: 0.8704 (pp20)
REVERT: b  127 ASP cc_start: 0.9141 (p0) cc_final: 0.8879 (p0)
REVERT: b  152 LEU cc_start: 0.9705 (tp) cc_final: 0.9484 (tp)
REVERT: b  185 TYR cc_start: 0.7620 (m-10) cc_final: 0.7238 (m-10)
REVERT: b  210 TYR cc_start: 0.8450 (m-80) cc_final: 0.7959 (m-80)
REVERT: b  217 LEU cc_start: 0.8528 (mt) cc_final: 0.8253 (mt)
REVERT: b  260 VAL cc_start: 0.8949 (t) cc_final: 0.8562 (p)
REVERT: b  313 MET cc_start: 0.7726 (mpp) cc_final: 0.7463 (mpp)
REVERT: g   22 TRP cc_start: 0.8472 (m100) cc_final: 0.7852 (m100)
REVERT: g  103 ASN cc_start: 0.7541 (m110) cc_final: 0.7290 (m110)
REVERT: g  169 TYR cc_start: 0.8158 (m-10) cc_final: 0.7832 (m-10)
REVERT: g  197 GLN cc_start: 0.9116 (mm-40) cc_final: 0.8809 (mm-40)
REVERT: g  206 ASP cc_start: 0.7906 (t0) cc_final: 0.7657 (t0)
REVERT: g  236 MET cc_start: 0.8843 (mmm) cc_final: 0.7792 (mmm)
REVERT: g  335 LYS cc_start: 0.9392 (mmpt) cc_final: 0.9169 (mmmt)
REVERT: g  392 CYS cc_start: 0.8352 (p) cc_final: 0.8128 (p)
REVERT: g  397 LYS cc_start: 0.8528 (tttt) cc_final: 0.8173 (mmmt)
REVERT: g  421 MET cc_start: 0.8980 (mtp) cc_final: 0.8695 (mtp)
REVERT: h   15 ASN cc_start: 0.8623 (m110) cc_final: 0.8216 (m110)
REVERT: h   20 GLU cc_start: 0.8262 (tp30) cc_final: 0.7707 (tp30)
REVERT: h  271 THR cc_start: 0.7612 (p) cc_final: 0.7356 (p)
REVERT: h  279 ASP cc_start: 0.7561 (m-30) cc_final: 0.7134 (t0)
REVERT: h  292 ASP cc_start: 0.9137 (p0) cc_final: 0.8911 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 318
  average time/residue: 0.2443
  time to fit residues: 119.1978
Evaluate side-chains
  259 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 1.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 139 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0870
   chunk 61 optimal weight:    0.6980
   chunk 93 optimal weight:    0.5980
   chunk 161 optimal weight:    3.9990
   chunk 147 optimal weight:    2.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
a 186 ASN
a 233 GLN
a 301 GLN
** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** g  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** g 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h  12 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 = 0.3346 r_free = 0.3346 target = 0.077802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.068402 restraints weight = 53902.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.070426 restraints weight = 32164.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.071890 restraints weight = 21378.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  13723  Z= 0.219
  Angle     :  0.608   7.506  18642  Z= 0.309
  Chirality :  0.044   0.154   2079
  Planarity :  0.004   0.044   2403
  Dihedral  :  9.382 156.247   1871
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.21), residues: 1647
  helix:  1.17 (0.19), residues: 770
  sheet: -1.22 (0.35), residues: 225
  loop : -0.75 (0.25), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP b  21 
 HIS   0.008   0.001   HIS g 115 
 PHE   0.021   0.001   PHE h  21 
 TYR   0.016   0.001   TYR g 169 
 ARG   0.004   0.000   ARG b 308 

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

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

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 313
  time to evaluate  : 1.652 
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: a   69 ASP cc_start: 0.6761 (m-30) cc_final: 0.6240 (m-30)
REVERT: a  196 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6975 (mm-30)
REVERT: a  280 LYS cc_start: 0.0948 (tptm) cc_final: 0.0743 (tptp)
REVERT: a  377 MET cc_start: 0.8833 (ttp) cc_final: 0.8604 (ttp)
REVERT: b   77 GLU cc_start: 0.9004 (pp20) cc_final: 0.8804 (pp20)
REVERT: b  152 LEU cc_start: 0.9698 (tp) cc_final: 0.9477 (tp)
REVERT: b  185 TYR cc_start: 0.7680 (m-10) cc_final: 0.7265 (m-10)
REVERT: b  187 SER cc_start: 0.9141 (m) cc_final: 0.8847 (p)
REVERT: b  210 TYR cc_start: 0.8289 (m-80) cc_final: 0.7741 (m-80)
REVERT: b  217 LEU cc_start: 0.8517 (mt) cc_final: 0.8251 (mt)
REVERT: b  260 VAL cc_start: 0.8938 (t) cc_final: 0.8521 (p)
REVERT: b  313 MET cc_start: 0.7748 (mpp) cc_final: 0.7507 (mpp)
REVERT: b  351 PHE cc_start: 0.8544 (m-80) cc_final: 0.7987 (m-80)
REVERT: g   22 TRP cc_start: 0.8495 (m100) cc_final: 0.7854 (m100)
REVERT: g  169 TYR cc_start: 0.8160 (m-80) cc_final: 0.7836 (m-10)
REVERT: g  197 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8805 (mm-40)
REVERT: g  236 MET cc_start: 0.8810 (mmm) cc_final: 0.7911 (mmm)
REVERT: g  253 LEU cc_start: 0.8910 (tp) cc_final: 0.8657 (tp)
REVERT: g  297 LEU cc_start: 0.8412 (mp) cc_final: 0.8062 (mp)
REVERT: g  335 LYS cc_start: 0.9424 (mmpt) cc_final: 0.9196 (mmmt)
REVERT: g  397 LYS cc_start: 0.8595 (tttt) cc_final: 0.8035 (mmmt)
REVERT: g  421 MET cc_start: 0.8988 (mtp) cc_final: 0.8725 (mtp)
REVERT: h   15 ASN cc_start: 0.8599 (m110) cc_final: 0.8204 (m110)
REVERT: h   20 GLU cc_start: 0.8216 (tp30) cc_final: 0.7649 (tp30)
REVERT: h  178 MET cc_start: 0.5118 (ttp) cc_final: 0.4265 (ttm)
REVERT: h  271 THR cc_start: 0.7916 (p) cc_final: 0.7475 (p)
REVERT: h  279 ASP cc_start: 0.7581 (m-30) cc_final: 0.7131 (t0)
REVERT: h  292 ASP cc_start: 0.9132 (p0) cc_final: 0.8844 (p0)
REVERT: h  377 MET cc_start: 0.8649 (ppp) cc_final: 0.8379 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 313
  average time/residue: 0.2202
  time to fit residues: 105.2037
Evaluate side-chains
  265 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 265
  time to evaluate  : 1.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 16 optimal weight:    0.4980
   chunk 82 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 106 optimal weight:    0.6980
   chunk 133 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 162 optimal weight:    0.5980
   chunk 72 optimal weight:    0.0470
   chunk 84 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
a 186 ASN
** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** g  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
g 103 ASN
** g 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
g 175 GLN
** h  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h 167 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 = 0.3363 r_free = 0.3363 target = 0.078638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.069121 restraints weight = 52906.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.071072 restraints weight = 31806.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.072606 restraints weight = 21282.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  13723  Z= 0.203
  Angle     :  0.608   7.824  18642  Z= 0.307
  Chirality :  0.044   0.182   2079
  Planarity :  0.004   0.043   2403
  Dihedral  :  9.256 155.453   1871
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.21), residues: 1647
  helix:  1.10 (0.18), residues: 771
  sheet: -1.05 (0.34), residues: 241
  loop : -0.58 (0.25), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP a  21 
 HIS   0.008   0.001   HIS g 115 
 PHE   0.022   0.001   PHE h  21 
 TYR   0.013   0.001   TYR b 161 
 ARG   0.004   0.000   ARG b 308 

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

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

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 319
  time to evaluate  : 1.679 
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   69 ASP cc_start: 0.6780 (m-30) cc_final: 0.6182 (m-30)
REVERT: a  293 ASN cc_start: 0.8942 (m-40) cc_final: 0.8717 (m110)
REVERT: a  302 MET cc_start: 0.8291 (mtm) cc_final: 0.8081 (mtm)
REVERT: a  415 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7347 (mt-10)
REVERT: b  152 LEU cc_start: 0.9730 (tp) cc_final: 0.9516 (tp)
REVERT: b  185 TYR cc_start: 0.7689 (m-10) cc_final: 0.7277 (m-10)
REVERT: b  210 TYR cc_start: 0.8200 (m-80) cc_final: 0.7600 (m-80)
REVERT: b  217 LEU cc_start: 0.8504 (mt) cc_final: 0.8244 (mt)
REVERT: b  260 VAL cc_start: 0.8989 (t) cc_final: 0.8594 (p)
REVERT: b  313 MET cc_start: 0.7710 (mpp) cc_final: 0.7412 (mpp)
REVERT: b  351 PHE cc_start: 0.8401 (m-80) cc_final: 0.7524 (m-10)
REVERT: g   22 TRP cc_start: 0.8406 (m100) cc_final: 0.7904 (m100)
REVERT: g  169 TYR cc_start: 0.8134 (m-80) cc_final: 0.7858 (m-10)
REVERT: g  197 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8850 (mm-40)
REVERT: g  234 THR cc_start: 0.8963 (m) cc_final: 0.8754 (m)
REVERT: g  236 MET cc_start: 0.8804 (mmm) cc_final: 0.7865 (mmm)
REVERT: g  297 LEU cc_start: 0.8494 (mp) cc_final: 0.8165 (mp)
REVERT: g  335 LYS cc_start: 0.9399 (mmpt) cc_final: 0.9184 (mmmt)
REVERT: g  397 LYS cc_start: 0.8619 (tttt) cc_final: 0.7969 (mmmt)
REVERT: g  421 MET cc_start: 0.8956 (mtp) cc_final: 0.8675 (mtp)
REVERT: h   15 ASN cc_start: 0.8609 (m110) cc_final: 0.8196 (m110)
REVERT: h   20 GLU cc_start: 0.8161 (tp30) cc_final: 0.7602 (tp30)
REVERT: h  178 MET cc_start: 0.5044 (ttp) cc_final: 0.4367 (ttm)
REVERT: h  279 ASP cc_start: 0.7526 (m-30) cc_final: 0.7115 (t0)
REVERT: h  292 ASP cc_start: 0.9162 (p0) cc_final: 0.8883 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 319
  average time/residue: 0.2347
  time to fit residues: 113.5872
Evaluate side-chains
  259 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 1.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 151 optimal weight:    0.3980
   chunk 38 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0030
   chunk 164 optimal weight:    0.9980
   chunk 137 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 109 optimal weight:    0.5980
   chunk 132 optimal weight:    4.9990
   overall best weight:    0.4790

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

Flipped N/Q/H residues before XYZ refinement:
a 186 ASN
** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
g 175 GLN
** g 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
h 167 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.078916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.069308 restraints weight = 52839.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.071342 restraints weight = 31819.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.072842 restraints weight = 21232.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.3196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13723  Z= 0.195
  Angle     :  0.621   8.252  18642  Z= 0.314
  Chirality :  0.044   0.186   2079
  Planarity :  0.004   0.042   2403
  Dihedral  :  9.129 155.089   1871
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.21), residues: 1647
  helix:  1.15 (0.19), residues: 767
  sheet: -1.20 (0.33), residues: 255
  loop : -0.47 (0.25), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP a  21 
 HIS   0.004   0.001   HIS h 115 
 PHE   0.019   0.001   PHE g 119 
 TYR   0.013   0.001   TYR b 319 
 ARG   0.003   0.000   ARG b 308 

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

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

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 318
  time to evaluate  : 1.582 
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   69 ASP cc_start: 0.6659 (m-30) cc_final: 0.6123 (m-30)
REVERT: a  186 ASN cc_start: 0.8682 (m-40) cc_final: 0.8461 (m110)
REVERT: a  254 ASP cc_start: 0.7541 (t70) cc_final: 0.7062 (t70)
REVERT: a  280 LYS cc_start: 0.0838 (tptm) cc_final: 0.0505 (tptp)
REVERT: a  293 ASN cc_start: 0.8988 (m-40) cc_final: 0.8740 (m110)
REVERT: a  302 MET cc_start: 0.8128 (mtm) cc_final: 0.7905 (mtm)
REVERT: a  377 MET cc_start: 0.8873 (ttp) cc_final: 0.8651 (ttp)
REVERT: b  137 VAL cc_start: 0.8728 (t) cc_final: 0.8468 (p)
REVERT: b  152 LEU cc_start: 0.9647 (tp) cc_final: 0.9443 (tp)
REVERT: b  183 GLU cc_start: 0.8545 (mp0) cc_final: 0.8115 (mp0)
REVERT: b  185 TYR cc_start: 0.7589 (m-10) cc_final: 0.7240 (m-10)
REVERT: b  187 SER cc_start: 0.9145 (m) cc_final: 0.8819 (p)
REVERT: b  217 LEU cc_start: 0.8505 (mt) cc_final: 0.8235 (mt)
REVERT: b  260 VAL cc_start: 0.8976 (t) cc_final: 0.8595 (p)
REVERT: b  313 MET cc_start: 0.7697 (mpp) cc_final: 0.7403 (mpp)
REVERT: g   22 TRP cc_start: 0.8381 (m100) cc_final: 0.7845 (m100)
REVERT: g  169 TYR cc_start: 0.8232 (m-80) cc_final: 0.7936 (m-10)
REVERT: g  197 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8854 (mm-40)
REVERT: g  206 ASP cc_start: 0.7892 (t0) cc_final: 0.7654 (t0)
REVERT: g  236 MET cc_start: 0.8812 (mmm) cc_final: 0.7941 (mmm)
REVERT: g  335 LYS cc_start: 0.9401 (mmpt) cc_final: 0.9186 (mmmt)
REVERT: g  397 LYS cc_start: 0.8577 (tttt) cc_final: 0.7839 (mmmt)
REVERT: g  421 MET cc_start: 0.8924 (mtp) cc_final: 0.8683 (mtp)
REVERT: h   15 ASN cc_start: 0.8578 (m110) cc_final: 0.8183 (m110)
REVERT: h   20 GLU cc_start: 0.8154 (tp30) cc_final: 0.7785 (tp30)
REVERT: h   22 TRP cc_start: 0.8748 (m100) cc_final: 0.8448 (m100)
REVERT: h  271 THR cc_start: 0.7947 (p) cc_final: 0.7438 (p)
REVERT: h  279 ASP cc_start: 0.7518 (m-30) cc_final: 0.7105 (t0)
REVERT: h  292 ASP cc_start: 0.9147 (p0) cc_final: 0.8864 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 318
  average time/residue: 0.2258
  time to fit residues: 108.4199
Evaluate side-chains
  260 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 1.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 119 optimal weight:    0.5980
   chunk 164 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 112 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0670
   chunk 36 optimal weight:    0.2980
   chunk 59 optimal weight:    1.9990
   chunk 131 optimal weight:    0.9980
   chunk 116 optimal weight:    0.2980
   overall best weight:    0.3918

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

Flipped N/Q/H residues before XYZ refinement:
** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
g  15 ASN
g 103 ASN
** g 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
g 175 GLN
** g 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h  12 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 = 0.3388 r_free = 0.3388 target = 0.079616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.069990 restraints weight = 52201.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.072030 restraints weight = 31599.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.073502 restraints weight = 21115.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.3400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13723  Z= 0.187
  Angle     :  0.623   8.554  18642  Z= 0.316
  Chirality :  0.045   0.321   2079
  Planarity :  0.004   0.042   2403
  Dihedral  :  8.992 153.909   1871
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.21), residues: 1647
  helix:  1.11 (0.18), residues: 777
  sheet: -1.12 (0.33), residues: 246
  loop : -0.56 (0.25), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP a  21 
 HIS   0.007   0.001   HIS a 192 
 PHE   0.022   0.001   PHE g 119 
 TYR   0.016   0.001   TYR b 172 
 ARG   0.003   0.000   ARG b 308 

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

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

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 311
  time to evaluate  : 1.724 
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   69 ASP cc_start: 0.6625 (m-30) cc_final: 0.6071 (m-30)
REVERT: a  280 LYS cc_start: 0.0854 (tptm) cc_final: 0.0598 (tptp)
REVERT: a  293 ASN cc_start: 0.8984 (m-40) cc_final: 0.8749 (m110)
REVERT: a  302 MET cc_start: 0.8033 (mtm) cc_final: 0.7759 (mtm)
REVERT: a  377 MET cc_start: 0.8796 (ttp) cc_final: 0.8483 (ttp)
REVERT: b   77 GLU cc_start: 0.8874 (pp20) cc_final: 0.8662 (pp20)
REVERT: b  137 VAL cc_start: 0.8774 (t) cc_final: 0.8548 (p)
REVERT: b  152 LEU cc_start: 0.9618 (tp) cc_final: 0.9348 (tp)
REVERT: b  183 GLU cc_start: 0.8567 (mp0) cc_final: 0.8094 (mp0)
REVERT: b  185 TYR cc_start: 0.7468 (m-10) cc_final: 0.7230 (m-10)
REVERT: b  187 SER cc_start: 0.9126 (m) cc_final: 0.8789 (p)
REVERT: b  217 LEU cc_start: 0.8434 (mt) cc_final: 0.8173 (mt)
REVERT: b  260 VAL cc_start: 0.9029 (t) cc_final: 0.8657 (p)
REVERT: b  303 VAL cc_start: 0.8986 (t) cc_final: 0.8696 (t)
REVERT: g   22 TRP cc_start: 0.8353 (m100) cc_final: 0.7817 (m100)
REVERT: g  116 GLU cc_start: 0.8015 (pm20) cc_final: 0.7693 (pm20)
REVERT: g  169 TYR cc_start: 0.8251 (m-80) cc_final: 0.7696 (m-10)
REVERT: g  197 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8815 (mm-40)
REVERT: g  206 ASP cc_start: 0.7752 (t0) cc_final: 0.7507 (t0)
REVERT: g  236 MET cc_start: 0.8763 (mmm) cc_final: 0.7845 (mmm)
REVERT: g  335 LYS cc_start: 0.9367 (mmpt) cc_final: 0.9158 (mmmt)
REVERT: g  397 LYS cc_start: 0.8486 (tttt) cc_final: 0.7711 (mmmt)
REVERT: g  421 MET cc_start: 0.8891 (mtp) cc_final: 0.8662 (mtp)
REVERT: h   15 ASN cc_start: 0.8575 (m110) cc_final: 0.8176 (m110)
REVERT: h   20 GLU cc_start: 0.8145 (tp30) cc_final: 0.7741 (tp30)
REVERT: h   22 TRP cc_start: 0.8758 (m100) cc_final: 0.8440 (m100)
REVERT: h  271 THR cc_start: 0.7879 (p) cc_final: 0.7231 (p)
REVERT: h  279 ASP cc_start: 0.7461 (m-30) cc_final: 0.7085 (t0)
REVERT: h  292 ASP cc_start: 0.9152 (p0) cc_final: 0.8865 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 311
  average time/residue: 0.2390
  time to fit residues: 111.6327
Evaluate side-chains
  258 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 1.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 106 optimal weight:    0.0040
   chunk 60 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 92 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 90 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
a 186 ASN
** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 197 HIS
b 216 ASN
g 103 ASN
** g 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** g 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
g 175 GLN
** g 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
h 167 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.078736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.069129 restraints weight = 52931.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.071131 restraints weight = 31916.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.072557 restraints weight = 21369.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.3411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13723  Z= 0.216
  Angle     :  0.646  10.139  18642  Z= 0.328
  Chirality :  0.045   0.242   2079
  Planarity :  0.004   0.042   2403
  Dihedral  :  8.990 154.426   1871
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.21), residues: 1647
  helix:  1.04 (0.19), residues: 777
  sheet: -1.13 (0.33), residues: 246
  loop : -0.56 (0.25), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP a  21 
 HIS   0.005   0.001   HIS a 192 
 PHE   0.022   0.002   PHE g 119 
 TYR   0.018   0.001   TYR b 210 
 ARG   0.006   0.000   ARG a 422 

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

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

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3294 Ramachandran restraints generated.
    1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 310
  time to evaluate  : 1.494 
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   69 ASP cc_start: 0.6692 (m-30) cc_final: 0.6106 (m-30)
REVERT: a  186 ASN cc_start: 0.8564 (m-40) cc_final: 0.8362 (m110)
REVERT: a  254 ASP cc_start: 0.7501 (t70) cc_final: 0.7204 (t70)
REVERT: a  293 ASN cc_start: 0.8993 (m-40) cc_final: 0.8756 (m110)
REVERT: a  302 MET cc_start: 0.8055 (mtm) cc_final: 0.7781 (mtm)
REVERT: b   77 GLU cc_start: 0.8911 (pp20) cc_final: 0.8683 (pp20)
REVERT: b  137 VAL cc_start: 0.8811 (t) cc_final: 0.8596 (p)
REVERT: b  152 LEU cc_start: 0.9615 (tp) cc_final: 0.9291 (tp)
REVERT: b  183 GLU cc_start: 0.8459 (mp0) cc_final: 0.8004 (mp0)
REVERT: b  185 TYR cc_start: 0.7613 (m-10) cc_final: 0.7355 (m-10)
REVERT: b  187 SER cc_start: 0.9111 (m) cc_final: 0.8786 (p)
REVERT: b  217 LEU cc_start: 0.8452 (mt) cc_final: 0.8196 (mt)
REVERT: b  260 VAL cc_start: 0.9063 (t) cc_final: 0.8708 (m)
REVERT: b  305 CYS cc_start: 0.8529 (m) cc_final: 0.8025 (m)
REVERT: g   20 GLU cc_start: 0.8375 (pm20) cc_final: 0.8073 (pm20)
REVERT: g   22 TRP cc_start: 0.8381 (m100) cc_final: 0.7928 (m100)
REVERT: g  205 LEU cc_start: 0.9103 (mt) cc_final: 0.8845 (mt)
REVERT: g  206 ASP cc_start: 0.7875 (t0) cc_final: 0.7615 (t0)
REVERT: g  236 MET cc_start: 0.8780 (mmm) cc_final: 0.8003 (mmm)
REVERT: g  335 LYS cc_start: 0.9395 (mmpt) cc_final: 0.9171 (mmmt)
REVERT: g  397 LYS cc_start: 0.8469 (tttt) cc_final: 0.7737 (mmmt)
REVERT: g  421 MET cc_start: 0.8914 (mtp) cc_final: 0.8688 (mtp)
REVERT: h   15 ASN cc_start: 0.8541 (m110) cc_final: 0.8163 (m110)
REVERT: h   20 GLU cc_start: 0.8181 (tp30) cc_final: 0.7802 (tp30)
REVERT: h   22 TRP cc_start: 0.8818 (m100) cc_final: 0.8470 (m100)
REVERT: h  271 THR cc_start: 0.7901 (p) cc_final: 0.7513 (p)
REVERT: h  279 ASP cc_start: 0.7521 (m-30) cc_final: 0.7124 (t0)
REVERT: h  292 ASP cc_start: 0.9136 (p0) cc_final: 0.8844 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 310
  average time/residue: 0.2365
  time to fit residues: 111.1139
Evaluate side-chains
  252 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 1.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0970
   chunk 18 optimal weight:    0.7980
   chunk 59 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 152 optimal weight:    0.9980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** g  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** g 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
g 175 GLN
g 197 GLN
** g 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h  12 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 = 0.3373 r_free = 0.3373 target = 0.079010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.069313 restraints weight = 53054.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.071305 restraints weight = 32241.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.072754 restraints weight = 21728.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.3478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13723  Z= 0.209
  Angle     :  0.637   8.644  18642  Z= 0.323
  Chirality :  0.045   0.230   2079
  Planarity :  0.004   0.042   2403
  Dihedral  :  8.948 154.611   1871
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.21), residues: 1647
  helix:  1.07 (0.19), residues: 778
  sheet: -1.08 (0.33), residues: 246
  loop : -0.56 (0.25), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP a  21 
 HIS   0.007   0.001   HIS g 115 
 PHE   0.020   0.001   PHE g 119 
 TYR   0.016   0.001   TYR b 399 
 ARG   0.005   0.000   ARG a 422 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3722.65 seconds
wall clock time: 68 minutes 19.10 seconds (4099.10 seconds total)