Starting phenix.real_space_refine
on Sat Aug 23 17:11:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8va2_43085/08_2025/8va2_43085.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8va2_43085/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8va2_43085/08_2025/8va2_43085.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8va2_43085/08_2025/8va2_43085.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8va2_43085/08_2025/8va2_43085.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8va2_43085/08_2025/8va2_43085.map"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 3.60, per 1000 atoms: 0.27
  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: 1.24
  Conformation dependent library (CDL) restraints added in 487.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.29
  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: 2.06

  Time building geometry restraints manager: 1.58 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 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:             4.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     12.750
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.850
-------------------------------------------------------------------------------
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= 0.290
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.34 (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
 ARG   0.012   0.000   ARG b 229 
 TYR   0.016   0.001   TYR b 399 
 PHE   0.016   0.001   PHE g 119 
 TRP   0.005   0.001   TRP g 351 
 HIS   0.006   0.001   HIS a  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00584 (13723)
  covalent geometry    : angle       0.87273 (18642)
  hydrogen bonds       : bond        0.15172 (  647)
  hydrogen bonds       : angle       6.57563 ( 1875)

*********************** 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  : 0.456 
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: 0.7798 (mmp)
REVERT: a  259 LEU cc_start: 0.9375 (mt) cc_final: 0.9154 (mt)
REVERT: a  377 MET cc_start: 0.8759 (ttp) cc_final: 0.8543 (ttp)
REVERT: b  152 LEU cc_start: 0.9639 (tp) cc_final: 0.9353 (tp)
REVERT: b  176 GLN cc_start: 0.8675 (mm110) cc_final: 0.8464 (mm-40)
REVERT: b  183 GLU cc_start: 0.8533 (mp0) cc_final: 0.8204 (mp0)
REVERT: b  185 TYR cc_start: 0.7832 (m-10) cc_final: 0.7218 (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: 0.7214 (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: 0.8654 (mpp)
REVERT: g  388 PHE cc_start: 0.8925 (m-10) cc_final: 0.8662 (m-10)
REVERT: g  397 LYS cc_start: 0.8700 (tttt) cc_final: 0.7994 (mmmt)
REVERT: g  421 MET cc_start: 0.9023 (mtp) cc_final: 0.8721 (mtp)
REVERT: h   15 ASN cc_start: 0.8452 (m110) cc_final: 0.8161 (m110)
REVERT: h   20 GLU cc_start: 0.8352 (tp30) cc_final: 0.7990 (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: 0.6997 (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: 0.8819 (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: 0.1093
  time to fit residues: 51.2633
Evaluate side-chains
  249 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    0.0370
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    1.9990
   overall best weight:    0.6058

-------------------------------------------------------------------------------
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
** b 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
g 197 GLN
** h   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
h 230 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.077397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.067979 restraints weight = 53369.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.069955 restraints weight = 31906.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.071442 restraints weight = 21418.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.072489 restraints weight = 15159.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.073284 restraints weight = 11313.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.1514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.089  13723  Z= 0.152
  Angle     :  0.617   7.209  18642  Z= 0.314
  Chirality :  0.045   0.207   2079
  Planarity :  0.004   0.054   2403
  Dihedral  : 10.837 179.482   1871
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  6.07 %
    Favored  : 93.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.21), residues: 1647
  helix:  1.24 (0.19), residues: 764
  sheet: -1.80 (0.32), residues: 241
  loop : -0.99 (0.25), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG b 229 
 TYR   0.015   0.001   TYR g 395 
 PHE   0.020   0.002   PHE h  21 
 TRP   0.008   0.001   TRP a 388 
 HIS   0.012   0.001   HIS h  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (13723)
  covalent geometry    : angle       0.61725 (18642)
  hydrogen bonds       : bond        0.04429 (  647)
  hydrogen bonds       : angle       5.35273 ( 1875)

*********************** 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
  324 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 319
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a  167 LEU cc_start: 0.9154 (mm) cc_final: 0.8842 (mm)
REVERT: a  203 MET cc_start: 0.8938 (mmp) cc_final: 0.7749 (mmp)
REVERT: a  254 ASP cc_start: 0.7503 (t70) cc_final: 0.6891 (t70)
REVERT: a  337 THR cc_start: 0.8431 (p) cc_final: 0.8213 (p)
REVERT: a  417 GLU cc_start: 0.8466 (mp0) cc_final: 0.8166 (mp0)
REVERT: b  185 TYR cc_start: 0.7737 (m-10) cc_final: 0.7302 (m-10)
REVERT: b  203 MET cc_start: 0.9464 (mmp) cc_final: 0.8484 (mmm)
REVERT: b  217 LEU cc_start: 0.8583 (mt) cc_final: 0.8238 (mt)
REVERT: b  254 ASP cc_start: 0.8714 (m-30) cc_final: 0.8487 (m-30)
REVERT: b  260 VAL cc_start: 0.8898 (t) cc_final: 0.8582 (m)
REVERT: b  301 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8386 (pt0)
REVERT: b  302 MET cc_start: 0.8900 (tpp) cc_final: 0.8695 (tpp)
REVERT: b  313 MET cc_start: 0.7314 (mtt) cc_final: 0.7072 (mpp)
REVERT: b  377 MET cc_start: 0.8692 (tmm) cc_final: 0.8157 (tmm)
REVERT: g   22 TRP cc_start: 0.8526 (m100) cc_final: 0.8198 (m100)
REVERT: g   52 PHE cc_start: 0.8587 (m-80) cc_final: 0.8375 (m-80)
REVERT: g  392 CYS cc_start: 0.8509 (p) cc_final: 0.8251 (p)
REVERT: g  397 LYS cc_start: 0.8730 (tttt) cc_final: 0.8282 (mmmt)
REVERT: h   15 ASN cc_start: 0.8518 (m110) cc_final: 0.8071 (m110)
REVERT: h   20 GLU cc_start: 0.8411 (tp30) cc_final: 0.8072 (tp30)
REVERT: h  154 LEU cc_start: 0.9067 (mt) cc_final: 0.8867 (mt)
REVERT: h  204 VAL cc_start: 0.9299 (t) cc_final: 0.9081 (t)
REVERT: h  270 MET cc_start: 0.7620 (ttt) cc_final: 0.7364 (ttt)
REVERT: h  271 THR cc_start: 0.7851 (p) cc_final: 0.7475 (p)
  outliers start: 5
  outliers final: 0
  residues processed: 322
  average time/residue: 0.1042
  time to fit residues: 51.3124
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  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 154 optimal weight:    0.8980
   chunk 94 optimal weight:    0.8980
   chunk 112 optimal weight:    0.8980
   chunk 142 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 111 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0040
   chunk 93 optimal weight:    0.7980
   chunk 106 optimal weight:    0.2980
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.5392

-------------------------------------------------------------------------------
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
b 309 HIS
** g  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
g 158 ASN
** g 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
g 197 GLN
** h   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
h 167 GLN
h 187 ASN
h 302 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.077725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.068357 restraints weight = 53287.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.070327 restraints weight = 31656.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.071823 restraints weight = 21057.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.072882 restraints weight = 14852.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.073643 restraints weight = 11030.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  13723  Z= 0.141
  Angle     :  0.601   6.429  18642  Z= 0.306
  Chirality :  0.045   0.245   2079
  Planarity :  0.004   0.051   2403
  Dihedral  :  9.991 166.019   1871
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  4.43 %
    Favored  : 95.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.21), residues: 1647
  helix:  1.22 (0.18), residues: 763
  sheet: -1.59 (0.32), residues: 240
  loop : -0.89 (0.25), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG a 320 
 TYR   0.016   0.001   TYR b 172 
 PHE   0.016   0.001   PHE h  51 
 TRP   0.011   0.001   TRP a  21 
 HIS   0.007   0.001   HIS h  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (13723)
  covalent geometry    : angle       0.60142 (18642)
  hydrogen bonds       : bond        0.04215 (  647)
  hydrogen bonds       : angle       5.19544 ( 1875)

*********************** 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
  322 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 319
  time to evaluate  : 0.584 
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: a  167 LEU cc_start: 0.9207 (mm) cc_final: 0.8891 (mm)
REVERT: a  196 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6812 (mm-30)
REVERT: a  203 MET cc_start: 0.8949 (mmp) cc_final: 0.7813 (mmp)
REVERT: a  293 ASN cc_start: 0.8828 (t0) cc_final: 0.8626 (t0)
REVERT: a  377 MET cc_start: 0.8743 (ttp) cc_final: 0.8414 (ttp)
REVERT: b  185 TYR cc_start: 0.7671 (m-10) cc_final: 0.7224 (m-10)
REVERT: b  203 MET cc_start: 0.9434 (mmp) cc_final: 0.8528 (mmm)
REVERT: b  210 TYR cc_start: 0.8429 (m-80) cc_final: 0.7946 (m-80)
REVERT: b  217 LEU cc_start: 0.8621 (mt) cc_final: 0.8325 (mt)
REVERT: b  260 VAL cc_start: 0.8907 (t) cc_final: 0.8487 (p)
REVERT: b  301 GLN cc_start: 0.8602 (tp-100) cc_final: 0.8357 (pt0)
REVERT: b  302 MET cc_start: 0.8819 (tpp) cc_final: 0.8587 (tpp)
REVERT: g   52 PHE cc_start: 0.8586 (m-80) cc_final: 0.8314 (m-80)
REVERT: g  198 ASN cc_start: 0.8017 (m-40) cc_final: 0.7468 (m-40)
REVERT: g  253 LEU cc_start: 0.8716 (tp) cc_final: 0.8233 (tp)
REVERT: g  377 MET cc_start: 0.8328 (tmm) cc_final: 0.7903 (tmm)
REVERT: g  392 CYS cc_start: 0.8468 (p) cc_final: 0.8224 (p)
REVERT: g  397 LYS cc_start: 0.8548 (tttt) cc_final: 0.7981 (mmmt)
REVERT: g  421 MET cc_start: 0.8981 (mtp) cc_final: 0.8695 (mtp)
REVERT: h   15 ASN cc_start: 0.8761 (m110) cc_final: 0.8427 (m110)
REVERT: h   20 GLU cc_start: 0.8492 (tp30) cc_final: 0.8146 (tp30)
REVERT: h  154 LEU cc_start: 0.9086 (mt) cc_final: 0.8865 (mt)
REVERT: h  155 GLU cc_start: 0.9138 (tt0) cc_final: 0.8656 (pt0)
REVERT: h  271 THR cc_start: 0.7783 (p) cc_final: 0.7505 (p)
  outliers start: 3
  outliers final: 0
  residues processed: 320
  average time/residue: 0.1086
  time to fit residues: 52.6946
Evaluate side-chains
  247 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 54 optimal weight:    0.5980
   chunk 110 optimal weight:    0.8980
   chunk 73 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0570
   chunk 98 optimal weight:    0.0270
   chunk 61 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 148 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.3956

-------------------------------------------------------------------------------
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
a 186 ASN
a 233 GLN
a 301 GLN
g  15 ASN
g 158 ASN
g 197 GLN
** h   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
h 302 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.078828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.069398 restraints weight = 52670.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.071409 restraints weight = 31459.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.072928 restraints weight = 21044.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.073984 restraints weight = 14840.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.074783 restraints weight = 11078.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  13723  Z= 0.125
  Angle     :  0.587   6.780  18642  Z= 0.297
  Chirality :  0.044   0.203   2079
  Planarity :  0.004   0.048   2403
  Dihedral  :  9.617 156.439   1871
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  4.37 %
    Favored  : 95.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.21), residues: 1647
  helix:  1.23 (0.18), residues: 765
  sheet: -1.40 (0.33), residues: 237
  loop : -0.73 (0.25), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG a 121 
 TYR   0.026   0.001   TYR g 169 
 PHE   0.021   0.001   PHE a 351 
 TRP   0.008   0.001   TRP b 346 
 HIS   0.007   0.001   HIS a 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (13723)
  covalent geometry    : angle       0.58693 (18642)
  hydrogen bonds       : bond        0.04031 (  647)
  hydrogen bonds       : angle       4.93504 ( 1875)

*********************** 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
  329 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 326
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a  155 GLU cc_start: 0.8538 (pp20) cc_final: 0.8333 (pp20)
REVERT: a  156 ARG cc_start: 0.9271 (tpp80) cc_final: 0.9022 (tpp80)
REVERT: a  167 LEU cc_start: 0.9038 (mm) cc_final: 0.8612 (mm)
REVERT: a  196 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6819 (mm-30)
REVERT: a  203 MET cc_start: 0.8945 (mmp) cc_final: 0.7842 (mmp)
REVERT: a  377 MET cc_start: 0.8831 (ttp) cc_final: 0.8578 (ttp)
REVERT: b   77 GLU cc_start: 0.8904 (pp20) cc_final: 0.8703 (pp20)
REVERT: b  152 LEU cc_start: 0.9639 (tp) cc_final: 0.9315 (tp)
REVERT: b  157 LEU cc_start: 0.9001 (mt) cc_final: 0.8786 (mt)
REVERT: b  185 TYR cc_start: 0.7591 (m-10) cc_final: 0.7249 (m-10)
REVERT: b  187 SER cc_start: 0.9135 (m) cc_final: 0.8805 (p)
REVERT: b  210 TYR cc_start: 0.8402 (m-80) cc_final: 0.7964 (m-80)
REVERT: b  217 LEU cc_start: 0.8469 (mt) cc_final: 0.8179 (mt)
REVERT: b  260 VAL cc_start: 0.8918 (t) cc_final: 0.8518 (p)
REVERT: b  301 GLN cc_start: 0.8627 (tp-100) cc_final: 0.8343 (pt0)
REVERT: b  302 MET cc_start: 0.8779 (tpp) cc_final: 0.8561 (tpp)
REVERT: g   22 TRP cc_start: 0.8451 (m100) cc_final: 0.8035 (m100)
REVERT: g  198 ASN cc_start: 0.7580 (m-40) cc_final: 0.7164 (m-40)
REVERT: g  377 MET cc_start: 0.8362 (tmm) cc_final: 0.7911 (tmm)
REVERT: g  392 CYS cc_start: 0.8337 (p) cc_final: 0.8133 (p)
REVERT: g  397 LYS cc_start: 0.8539 (tttt) cc_final: 0.8151 (mmmt)
REVERT: g  421 MET cc_start: 0.8950 (mtp) cc_final: 0.8660 (mtp)
REVERT: h   15 ASN cc_start: 0.8629 (m110) cc_final: 0.8238 (m110)
REVERT: h   20 GLU cc_start: 0.8354 (tp30) cc_final: 0.7878 (tp30)
REVERT: h  154 LEU cc_start: 0.9098 (mt) cc_final: 0.8859 (mt)
REVERT: h  155 GLU cc_start: 0.9157 (tt0) cc_final: 0.8644 (pt0)
REVERT: h  271 THR cc_start: 0.7780 (p) cc_final: 0.7526 (p)
REVERT: h  292 ASP cc_start: 0.9121 (p0) cc_final: 0.8909 (p0)
  outliers start: 3
  outliers final: 0
  residues processed: 327
  average time/residue: 0.1081
  time to fit residues: 53.5380
Evaluate side-chains
  262 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 77 optimal weight:    4.9990
   chunk 117 optimal weight:    0.1980
   chunk 8 optimal weight:    2.9990
   chunk 120 optimal weight:    0.3980
   chunk 135 optimal weight:    0.1980
   chunk 163 optimal weight:    0.6980
   chunk 61 optimal weight:    0.1980
   chunk 88 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    0.3380

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

Flipped N/Q/H residues before XYZ refinement:
a  61 HIS
a 186 ASN
** a 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
a 301 GLN
** g 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
g 197 GLN
** g 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h   9 GLN ** 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.079849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.070427 restraints weight = 52730.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.072457 restraints weight = 31533.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.073924 restraints weight = 21065.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.074956 restraints weight = 14935.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.075743 restraints weight = 11215.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  13723  Z= 0.126
  Angle     :  0.612  10.345  18642  Z= 0.307
  Chirality :  0.044   0.181   2079
  Planarity :  0.004   0.046   2403
  Dihedral  :  9.409 155.212   1871
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.25 %
    Favored  : 97.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.21), residues: 1647
  helix:  1.19 (0.19), residues: 768
  sheet: -1.08 (0.35), residues: 219
  loop : -0.75 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG b 308 
 TYR   0.027   0.001   TYR g 169 
 PHE   0.031   0.001   PHE a 351 
 TRP   0.007   0.001   TRP a  21 
 HIS   0.007   0.001   HIS h 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (13723)
  covalent geometry    : angle       0.61226 (18642)
  hydrogen bonds       : bond        0.03911 (  647)
  hydrogen bonds       : angle       4.95099 ( 1875)

*********************** 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
  326 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 325
  time to evaluate  : 0.541 
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: 0.9107 (mm) cc_final: 0.8718 (mm)
REVERT: b  152 LEU cc_start: 0.9484 (tp) cc_final: 0.9253 (tp)
REVERT: b  185 TYR cc_start: 0.7561 (m-10) cc_final: 0.7220 (m-10)
REVERT: b  187 SER cc_start: 0.9130 (m) cc_final: 0.8787 (p)
REVERT: b  217 LEU cc_start: 0.8502 (mt) cc_final: 0.8231 (mt)
REVERT: b  260 VAL cc_start: 0.8934 (t) cc_final: 0.8552 (p)
REVERT: b  301 GLN cc_start: 0.8651 (tp-100) cc_final: 0.8371 (pt0)
REVERT: b  302 MET cc_start: 0.8736 (tpp) cc_final: 0.8415 (tpp)
REVERT: b  313 MET cc_start: 0.7848 (mpp) cc_final: 0.7622 (mpp)
REVERT: g   22 TRP cc_start: 0.8432 (m100) cc_final: 0.7852 (m100)
REVERT: g  103 ASN cc_start: 0.7395 (m110) cc_final: 0.7003 (m-40)
REVERT: g  234 THR cc_start: 0.8956 (m) cc_final: 0.8713 (m)
REVERT: g  253 LEU cc_start: 0.8910 (tp) cc_final: 0.8633 (tp)
REVERT: g  377 MET cc_start: 0.8284 (tmm) cc_final: 0.7817 (tmm)
REVERT: g  392 CYS cc_start: 0.8318 (p) cc_final: 0.8090 (p)
REVERT: g  397 LYS cc_start: 0.8467 (tttt) cc_final: 0.8091 (mmmt)
REVERT: g  421 MET cc_start: 0.8921 (mtp) cc_final: 0.8651 (mtp)
REVERT: h   20 GLU cc_start: 0.8233 (tp30) cc_final: 0.7658 (tp30)
REVERT: h   85 LEU cc_start: 0.9354 (tp) cc_final: 0.9097 (tp)
REVERT: h  271 THR cc_start: 0.7681 (p) cc_final: 0.7227 (p)
REVERT: h  279 ASP cc_start: 0.7394 (m-30) cc_final: 0.7134 (t70)
REVERT: h  292 ASP cc_start: 0.9113 (p0) cc_final: 0.8892 (p0)
REVERT: h  377 MET cc_start: 0.8577 (ppp) cc_final: 0.8264 (ppp)
  outliers start: 1
  outliers final: 0
  residues processed: 326
  average time/residue: 0.1036
  time to fit residues: 51.9764
Evaluate side-chains
  261 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 128 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 145 optimal weight:    0.9990
   chunk 142 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   chunk 53 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 154 optimal weight:    0.8980
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
a  11 GLN
a  18 ASN
a 186 ASN
** a 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 380 ASN
g  15 ASN
g 175 GLN
g 197 GLN
g 198 ASN
** h   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.077196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.067811 restraints weight = 53452.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.069777 restraints weight = 31741.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.071248 restraints weight = 21324.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.072272 restraints weight = 15132.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.073052 restraints weight = 11318.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087  13723  Z= 0.175
  Angle     :  0.633   8.952  18642  Z= 0.324
  Chirality :  0.045   0.209   2079
  Planarity :  0.004   0.062   2403
  Dihedral  :  9.403 156.789   1871
  Min Nonbonded Distance : 1.863

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.93 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.21), residues: 1647
  helix:  1.15 (0.18), residues: 769
  sheet: -1.01 (0.34), residues: 225
  loop : -0.76 (0.25), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG a 121 
 TYR   0.044   0.002   TYR g 169 
 PHE   0.020   0.002   PHE h  21 
 TRP   0.008   0.001   TRP h 351 
 HIS   0.007   0.001   HIS g 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (13723)
  covalent geometry    : angle       0.63332 (18642)
  hydrogen bonds       : bond        0.04162 (  647)
  hydrogen bonds       : angle       5.06146 ( 1875)

*********************** 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
  304 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 303
  time to evaluate  : 0.670 
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  377 MET cc_start: 0.8848 (ttp) cc_final: 0.8577 (ttp)
REVERT: a  415 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7460 (mt-10)
REVERT: b  152 LEU cc_start: 0.9509 (tp) cc_final: 0.9290 (tp)
REVERT: b  157 LEU cc_start: 0.9031 (mt) cc_final: 0.8821 (mt)
REVERT: b  185 TYR cc_start: 0.7673 (m-10) cc_final: 0.7243 (m-10)
REVERT: b  187 SER cc_start: 0.9187 (m) cc_final: 0.8878 (p)
REVERT: b  217 LEU cc_start: 0.8548 (mt) cc_final: 0.8269 (mt)
REVERT: b  260 VAL cc_start: 0.8882 (t) cc_final: 0.8465 (p)
REVERT: b  301 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8390 (pt0)
REVERT: b  302 MET cc_start: 0.8839 (tpp) cc_final: 0.8550 (tpp)
REVERT: b  313 MET cc_start: 0.7634 (mpp) cc_final: 0.7396 (mpp)
REVERT: b  351 PHE cc_start: 0.8529 (m-80) cc_final: 0.7952 (m-80)
REVERT: g  103 ASN cc_start: 0.7571 (m110) cc_final: 0.7356 (m110)
REVERT: g  236 MET cc_start: 0.8793 (mmm) cc_final: 0.7706 (mmm)
REVERT: g  377 MET cc_start: 0.8523 (tmm) cc_final: 0.8108 (tmm)
REVERT: g  397 LYS cc_start: 0.8578 (tttt) cc_final: 0.7989 (mmmt)
REVERT: g  421 MET cc_start: 0.8985 (mtp) cc_final: 0.8728 (mtp)
REVERT: h   15 ASN cc_start: 0.8965 (m110) cc_final: 0.8556 (m110)
REVERT: h   20 GLU cc_start: 0.8293 (tp30) cc_final: 0.7725 (tp30)
REVERT: h  178 MET cc_start: 0.5094 (ttp) cc_final: 0.4532 (ttm)
REVERT: h  279 ASP cc_start: 0.7484 (m-30) cc_final: 0.7076 (t0)
REVERT: h  292 ASP cc_start: 0.9132 (p0) cc_final: 0.8849 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 304
  average time/residue: 0.1040
  time to fit residues: 48.7462
Evaluate side-chains
  245 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 107 optimal weight:    0.0060
   chunk 83 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0770
   chunk 112 optimal weight:    0.0970
   chunk 71 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 14 optimal weight:    0.3980
   chunk 24 optimal weight:    0.6980
   chunk 119 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.2352

-------------------------------------------------------------------------------
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
** g 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
g 174 ASN
g 175 GLN
g 197 GLN
** h   9 GLN ** 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 = 0.3382 r_free = 0.3382 target = 0.079865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.070427 restraints weight = 51920.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.072437 restraints weight = 31107.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.073899 restraints weight = 20697.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.074977 restraints weight = 14757.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.075688 restraints weight = 11038.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.3234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  13723  Z= 0.121
  Angle     :  0.612   8.014  18642  Z= 0.310
  Chirality :  0.045   0.199   2079
  Planarity :  0.004   0.043   2403
  Dihedral  :  9.184 154.297   1871
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.25 %
    Favored  : 97.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.21), residues: 1647
  helix:  1.09 (0.18), residues: 780
  sheet: -0.84 (0.34), residues: 233
  loop : -0.68 (0.25), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG a 214 
 TYR   0.039   0.001   TYR g 169 
 PHE   0.021   0.001   PHE g 119 
 TRP   0.016   0.001   TRP a  21 
 HIS   0.007   0.001   HIS h 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (13723)
  covalent geometry    : angle       0.61208 (18642)
  hydrogen bonds       : bond        0.03916 (  647)
  hydrogen bonds       : angle       4.90988 ( 1875)

*********************** 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
  316 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 315
  time to evaluate  : 0.544 
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  280 LYS cc_start: -0.0518 (tptm) cc_final: -0.0933 (tptm)
REVERT: a  377 MET cc_start: 0.8630 (ttp) cc_final: 0.8162 (ttp)
REVERT: a  415 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7259 (mt-10)
REVERT: b  138 PHE cc_start: 0.8937 (m-80) cc_final: 0.8685 (m-10)
REVERT: b  152 LEU cc_start: 0.9496 (tp) cc_final: 0.9251 (tp)
REVERT: b  183 GLU cc_start: 0.8647 (mp0) cc_final: 0.8383 (mp0)
REVERT: b  185 TYR cc_start: 0.7712 (m-10) cc_final: 0.7364 (m-10)
REVERT: b  187 SER cc_start: 0.9175 (m) cc_final: 0.8866 (p)
REVERT: b  217 LEU cc_start: 0.8496 (mt) cc_final: 0.8197 (mt)
REVERT: b  260 VAL cc_start: 0.8937 (t) cc_final: 0.8537 (p)
REVERT: b  301 GLN cc_start: 0.8587 (tp-100) cc_final: 0.8326 (pt0)
REVERT: b  302 MET cc_start: 0.8686 (tpp) cc_final: 0.8467 (tpp)
REVERT: b  313 MET cc_start: 0.7714 (mpp) cc_final: 0.7399 (mpp)
REVERT: b  351 PHE cc_start: 0.8447 (m-80) cc_final: 0.7758 (m-10)
REVERT: g   22 TRP cc_start: 0.8431 (m100) cc_final: 0.7939 (m100)
REVERT: g  236 MET cc_start: 0.8734 (mmm) cc_final: 0.7114 (mmm)
REVERT: g  377 MET cc_start: 0.8301 (tmm) cc_final: 0.8071 (tmm)
REVERT: g  397 LYS cc_start: 0.8622 (tttt) cc_final: 0.7912 (mmmt)
REVERT: g  421 MET cc_start: 0.8901 (mtp) cc_final: 0.8693 (mtp)
REVERT: h   15 ASN cc_start: 0.9005 (m110) cc_final: 0.8661 (m110)
REVERT: h  178 MET cc_start: 0.4851 (ttp) cc_final: 0.4220 (ttm)
REVERT: h  193 LYS cc_start: 0.9356 (tptp) cc_final: 0.8925 (tttm)
REVERT: h  271 THR cc_start: 0.7741 (p) cc_final: 0.7136 (p)
REVERT: h  279 ASP cc_start: 0.7426 (m-30) cc_final: 0.7069 (t0)
REVERT: h  292 ASP cc_start: 0.9113 (p0) cc_final: 0.8843 (p0)
  outliers start: 1
  outliers final: 1
  residues processed: 316
  average time/residue: 0.1048
  time to fit residues: 50.7065
Evaluate side-chains
  264 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 263
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 147 optimal weight:    1.9990
   chunk 130 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 138 optimal weight:    0.7980
   chunk 70 optimal weight:    4.9990
   chunk 158 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   chunk 142 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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
g  15 ASN
g 175 GLN
** h   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.078144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.068772 restraints weight = 52988.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.070761 restraints weight = 32039.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.072206 restraints weight = 21490.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.073213 restraints weight = 15363.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.073972 restraints weight = 11599.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.3302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087  13723  Z= 0.161
  Angle     :  0.641  10.456  18642  Z= 0.328
  Chirality :  0.045   0.255   2079
  Planarity :  0.004   0.042   2403
  Dihedral  :  9.139 155.820   1871
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.21), residues: 1647
  helix:  1.01 (0.18), residues: 780
  sheet: -1.04 (0.34), residues: 249
  loop : -0.61 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG a 214 
 TYR   0.025   0.002   TYR g 169 
 PHE   0.019   0.002   PHE h 119 
 TRP   0.021   0.002   TRP a  21 
 HIS   0.007   0.001   HIS g 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (13723)
  covalent geometry    : angle       0.64112 (18642)
  hydrogen bonds       : bond        0.04166 (  647)
  hydrogen bonds       : angle       5.06620 ( 1875)

*********************** 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
  311 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 311
  time to evaluate  : 0.544 
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  377 MET cc_start: 0.8798 (ttp) cc_final: 0.8530 (ttp)
REVERT: a  415 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7319 (mt-10)
REVERT: b  152 LEU cc_start: 0.9501 (tp) cc_final: 0.9280 (tp)
REVERT: b  157 LEU cc_start: 0.9142 (mt) cc_final: 0.8940 (mt)
REVERT: b  185 TYR cc_start: 0.7557 (m-10) cc_final: 0.7254 (m-10)
REVERT: b  187 SER cc_start: 0.9172 (m) cc_final: 0.8841 (p)
REVERT: b  211 ASP cc_start: 0.8748 (t0) cc_final: 0.8535 (t0)
REVERT: b  217 LEU cc_start: 0.8534 (mt) cc_final: 0.8244 (mt)
REVERT: b  260 VAL cc_start: 0.8923 (t) cc_final: 0.8496 (p)
REVERT: b  301 GLN cc_start: 0.8607 (tp-100) cc_final: 0.8314 (pt0)
REVERT: b  302 MET cc_start: 0.8731 (tpp) cc_final: 0.8468 (tpp)
REVERT: b  313 MET cc_start: 0.7669 (mpp) cc_final: 0.7392 (mpp)
REVERT: b  351 PHE cc_start: 0.8454 (m-80) cc_final: 0.7361 (m-10)
REVERT: g   22 TRP cc_start: 0.8433 (m100) cc_final: 0.7982 (m100)
REVERT: g   58 GLU cc_start: 0.8338 (tp30) cc_final: 0.8022 (tp30)
REVERT: g  178 MET cc_start: 0.8428 (tpp) cc_final: 0.7946 (tpp)
REVERT: g  377 MET cc_start: 0.8421 (tmm) cc_final: 0.8037 (tmm)
REVERT: g  397 LYS cc_start: 0.8567 (tttt) cc_final: 0.7814 (mmmt)
REVERT: g  421 MET cc_start: 0.8909 (mtp) cc_final: 0.8556 (mtp)
REVERT: h   15 ASN cc_start: 0.8860 (m110) cc_final: 0.8491 (m110)
REVERT: h   20 GLU cc_start: 0.8507 (tp30) cc_final: 0.8133 (tp30)
REVERT: h  178 MET cc_start: 0.5036 (ttp) cc_final: 0.4402 (ttm)
REVERT: h  193 LYS cc_start: 0.9296 (tptp) cc_final: 0.8982 (tptm)
REVERT: h  271 THR cc_start: 0.7835 (p) cc_final: 0.7394 (p)
REVERT: h  279 ASP cc_start: 0.7472 (m-30) cc_final: 0.7107 (t0)
REVERT: h  292 ASP cc_start: 0.9145 (p0) cc_final: 0.8846 (p0)
REVERT: h  322 ASN cc_start: 0.7528 (t0) cc_final: 0.7315 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 311
  average time/residue: 0.1063
  time to fit residues: 50.6535
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  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 130 optimal weight:    0.5980
   chunk 65 optimal weight:    0.0970
   chunk 51 optimal weight:    0.8980
   chunk 163 optimal weight:    0.9990
   chunk 103 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 147 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 78 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   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 186 ASN
a 356 ASN
g 197 GLN
** g 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3362 r_free = 0.3362 target = 0.078872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.069397 restraints weight = 53612.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.071392 restraints weight = 32385.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.072869 restraints weight = 21683.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.073922 restraints weight = 15423.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.074703 restraints weight = 11604.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.3386

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= 0.151
  Angle     :  0.643  11.366  18642  Z= 0.328
  Chirality :  0.046   0.322   2079
  Planarity :  0.004   0.042   2403
  Dihedral  :  9.093 155.338   1871
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.21), residues: 1647
  helix:  1.01 (0.18), residues: 784
  sheet: -0.85 (0.34), residues: 236
  loop : -0.74 (0.25), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG a 214 
 TYR   0.015   0.001   TYR a 108 
 PHE   0.019   0.001   PHE g 119 
 TRP   0.030   0.002   TRP a  21 
 HIS   0.005   0.001   HIS g 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (13723)
  covalent geometry    : angle       0.64312 (18642)
  hydrogen bonds       : bond        0.04133 (  647)
  hydrogen bonds       : angle       5.11685 ( 1875)

*********************** 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
  309 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 309
  time to evaluate  : 0.588 
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  377 MET cc_start: 0.8699 (ttp) cc_final: 0.8299 (ttp)
REVERT: a  415 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7413 (mt-10)
REVERT: b  152 LEU cc_start: 0.9494 (tp) cc_final: 0.9262 (tp)
REVERT: b  157 LEU cc_start: 0.9116 (mt) cc_final: 0.8900 (mt)
REVERT: b  183 GLU cc_start: 0.8618 (mp0) cc_final: 0.8242 (mp0)
REVERT: b  185 TYR cc_start: 0.7488 (m-10) cc_final: 0.7175 (m-10)
REVERT: b  187 SER cc_start: 0.9153 (m) cc_final: 0.8831 (p)
REVERT: b  217 LEU cc_start: 0.8506 (mt) cc_final: 0.8236 (mt)
REVERT: b  260 VAL cc_start: 0.8903 (t) cc_final: 0.8454 (p)
REVERT: b  301 GLN cc_start: 0.8656 (tp-100) cc_final: 0.8383 (pt0)
REVERT: b  302 MET cc_start: 0.8685 (tpp) cc_final: 0.8376 (tpp)
REVERT: b  313 MET cc_start: 0.7663 (mpp) cc_final: 0.7419 (mpp)
REVERT: b  351 PHE cc_start: 0.8453 (m-10) cc_final: 0.7399 (m-10)
REVERT: g   22 TRP cc_start: 0.8425 (m100) cc_final: 0.7985 (m100)
REVERT: g  120 ASP cc_start: 0.8517 (m-30) cc_final: 0.8308 (m-30)
REVERT: g  174 ASN cc_start: 0.7486 (p0) cc_final: 0.7198 (p0)
REVERT: g  270 MET cc_start: 0.7754 (mtm) cc_final: 0.7544 (ptp)
REVERT: g  397 LYS cc_start: 0.8477 (tttt) cc_final: 0.7697 (mmmt)
REVERT: h   15 ASN cc_start: 0.8823 (m110) cc_final: 0.8456 (m110)
REVERT: h   20 GLU cc_start: 0.8418 (tp30) cc_final: 0.8036 (tp30)
REVERT: h  178 MET cc_start: 0.4962 (ttp) cc_final: 0.4414 (ttm)
REVERT: h  193 LYS cc_start: 0.9282 (tptp) cc_final: 0.8937 (tttm)
REVERT: h  271 THR cc_start: 0.7932 (p) cc_final: 0.7285 (p)
REVERT: h  279 ASP cc_start: 0.7457 (m-30) cc_final: 0.6948 (t0)
REVERT: h  292 ASP cc_start: 0.9122 (p0) cc_final: 0.8826 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 309
  average time/residue: 0.0984
  time to fit residues: 47.5183
Evaluate side-chains
  253 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 253
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 56 optimal weight:    0.3980
   chunk 19 optimal weight:    0.5980
   chunk 148 optimal weight:    0.9990
   chunk 115 optimal weight:    0.9980
   chunk 89 optimal weight:    0.2980
   chunk 8 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 155 optimal weight:    0.5980
   chunk 106 optimal weight:    0.0470
   chunk 131 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0070
   overall best weight:    0.2696

-------------------------------------------------------------------------------
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
** g  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
g 175 GLN
g 197 GLN
** g 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h   9 GLN ** 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.080827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.071175 restraints weight = 52362.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.073214 restraints weight = 31553.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.074721 restraints weight = 21165.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.075855 restraints weight = 15069.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.076627 restraints weight = 11234.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.3645

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= 0.123
  Angle     :  0.630  10.359  18642  Z= 0.318
  Chirality :  0.045   0.270   2079
  Planarity :  0.004   0.042   2403
  Dihedral  :  8.896 153.190   1871
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.21), residues: 1647
  helix:  1.09 (0.19), residues: 780
  sheet: -1.13 (0.32), residues: 244
  loop : -0.64 (0.25), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG a 214 
 TYR   0.016   0.001   TYR b 399 
 PHE   0.023   0.001   PHE g 119 
 TRP   0.022   0.002   TRP a  21 
 HIS   0.007   0.001   HIS g 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (13723)
  covalent geometry    : angle       0.63003 (18642)
  hydrogen bonds       : bond        0.03924 (  647)
  hydrogen bonds       : angle       5.02230 ( 1875)

********************** 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
  316 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 316
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a  186 ASN cc_start: 0.8573 (m-40) cc_final: 0.8360 (m110)
REVERT: a  254 ASP cc_start: 0.7606 (t70) cc_final: 0.7150 (t70)
REVERT: a  377 MET cc_start: 0.8905 (ttp) cc_final: 0.8547 (ttp)
REVERT: a  415 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7088 (mt-10)
REVERT: b  183 GLU cc_start: 0.8616 (mp0) cc_final: 0.8223 (mp0)
REVERT: b  185 TYR cc_start: 0.7461 (m-10) cc_final: 0.7230 (m-10)
REVERT: b  187 SER cc_start: 0.9131 (m) cc_final: 0.8816 (p)
REVERT: b  203 MET cc_start: 0.9309 (mmp) cc_final: 0.8173 (mmm)
REVERT: b  217 LEU cc_start: 0.8474 (mt) cc_final: 0.8177 (mt)
REVERT: b  260 VAL cc_start: 0.8990 (t) cc_final: 0.8566 (p)
REVERT: b  301 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8306 (pt0)
REVERT: b  302 MET cc_start: 0.8677 (tpp) cc_final: 0.8432 (tpp)
REVERT: b  313 MET cc_start: 0.7749 (mpp) cc_final: 0.7442 (mpp)
REVERT: b  351 PHE cc_start: 0.8352 (m-10) cc_final: 0.7302 (m-10)
REVERT: g   22 TRP cc_start: 0.8270 (m100) cc_final: 0.7786 (m100)
REVERT: g   58 GLU cc_start: 0.8222 (tp30) cc_final: 0.7934 (tp30)
REVERT: g  103 ASN cc_start: 0.7465 (m-40) cc_final: 0.7256 (m-40)
REVERT: g  116 GLU cc_start: 0.7982 (pm20) cc_final: 0.7712 (pm20)
REVERT: g  270 MET cc_start: 0.8003 (mtm) cc_final: 0.7662 (ptp)
REVERT: g  397 LYS cc_start: 0.8408 (tttt) cc_final: 0.7575 (mmmt)
REVERT: g  421 MET cc_start: 0.8762 (mtp) cc_final: 0.8517 (mtp)
REVERT: h   15 ASN cc_start: 0.9031 (m110) cc_final: 0.8614 (m110)
REVERT: h  178 MET cc_start: 0.4817 (ttp) cc_final: 0.4296 (ttm)
REVERT: h  193 LYS cc_start: 0.9314 (tptp) cc_final: 0.8898 (tttm)
REVERT: h  271 THR cc_start: 0.7665 (p) cc_final: 0.7309 (p)
REVERT: h  279 ASP cc_start: 0.7478 (m-30) cc_final: 0.7114 (t0)
REVERT: h  292 ASP cc_start: 0.9124 (p0) cc_final: 0.8812 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 316
  average time/residue: 0.1078
  time to fit residues: 51.9892
Evaluate side-chains
  263 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 132 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 127 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 108 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
a  11 GLN
b 216 ASN
g 175 GLN
g 197 GLN
** g 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.078022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.068563 restraints weight = 53417.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.070478 restraints weight = 32310.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.071901 restraints weight = 21676.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.072935 restraints weight = 15619.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.073668 restraints weight = 11822.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.3540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13723  Z= 0.176
  Angle     :  0.664  12.973  18642  Z= 0.339
  Chirality :  0.046   0.342   2079
  Planarity :  0.004   0.050   2403
  Dihedral  :  8.985 155.646   1871
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.21), residues: 1647
  helix:  0.96 (0.19), residues: 782
  sheet: -0.92 (0.34), residues: 238
  loop : -0.72 (0.25), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG a 214 
 TYR   0.014   0.002   TYR g 395 
 PHE   0.020   0.002   PHE h  21 
 TRP   0.032   0.002   TRP a  21 
 HIS   0.005   0.001   HIS h  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (13723)
  covalent geometry    : angle       0.66433 (18642)
  hydrogen bonds       : bond        0.04271 (  647)
  hydrogen bonds       : angle       5.17472 ( 1875)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2090.76 seconds
wall clock time: 37 minutes 33.76 seconds (2253.76 seconds total)