Starting phenix.real_space_refine
on Tue Jan 13 22:01:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jpc_36475/01_2026/8jpc_36475_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jpc_36475/01_2026/8jpc_36475.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jpc_36475/01_2026/8jpc_36475_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jpc_36475/01_2026/8jpc_36475_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jpc_36475/01_2026/8jpc_36475.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jpc_36475/01_2026/8jpc_36475.map"
  }
  resolution = 3.07
  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=   0.003 sd=   0.056
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: 8
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     P       2      5.49       5
     Mg      1      5.21       5
     S      55      5.16       5
     C    6155      2.51       5
     N    1638      2.21       5
     O    1732      1.98       5
     F       5      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9589
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "L"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 58
          Classifications: {'peptide': 6}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 4}
    Chain: "R"
      Number of atoms: 2111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2111
          Classifications: {'peptide': 297}
          Incomplete info: {'truncation_to_alanine': 63}
          Link IDs: {'PTRANS': 10, 'TRANS': 286}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 265
          Unresolved non-hydrogen angles: 339
          Unresolved non-hydrogen dihedrals: 231
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 5, 'PHE:plan': 5, 'HIS:plan': 4, 'TRP:plan': 1, 'ARG:plan': 7, 'GLU:plan': 1, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 156
    Chain: "G"
      Number of atoms: 5163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 658, 5163
          Classifications: {'peptide': 658}
          Incomplete info: {'truncation_to_alanine': 50}
          Link IDs: {'PTRANS': 28, 'TRANS': 629}
          Unresolved non-hydrogen bonds: 197
          Unresolved non-hydrogen angles: 240
          Unresolved non-hydrogen dihedrals: 161
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 12, 'ASP:plan': 8, 'GLN:plan1': 4, 'HIS:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 128
    Chain: "Q"
      Number of atoms: 2155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 2155
          Classifications: {'peptide': 317}
          Incomplete info: {'truncation_to_alanine': 118}
          Link IDs: {'PTRANS': 11, 'TRANS': 305}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 476
          Unresolved non-hydrogen angles: 598
          Unresolved non-hydrogen dihedrals: 396
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'GLU:plan': 18, 'ASP:plan': 14, 'ARG:plan': 11, 'PHE:plan': 5, 'GLN:plan1': 9, 'TYR:plan': 6, 'HIS:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 328
    Chain: "R"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 33
          Unusual residues: {'SRW': 1}
          Classifications: {'undetermined': 1}
    Chain: "G"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'STU': 1}
          Classifications: {'undetermined': 1}
    Chain: "Q"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "Q"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 6
          Unusual residues: {' MG': 1, 'ALF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.43, per 1000 atoms: 0.25
  Number of scatterers: 9589
  At special positions: 0
  Unit cell: (107.12, 106.296, 172.216, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      55     16.00
     P       2     15.00
     Al      1     13.00
     Mg      1     11.99
     F       5      9.00
     O    1732      8.00
     N    1638      7.00
     C    6155      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 141 " - pdb=" SG  CYS R 224 " distance=2.29

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.83
  Conformation dependent library (CDL) restraints added in 488.9 milliseconds
  

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2434

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 5 sheets defined
      63.9% alpha, 8.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'R' and resid 59 through 88
      removed outlier: 3.702A  pdb=" N   THR R  67 " --> pdb=" O   LYS R  63 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   VAL R  76 " --> pdb=" O   ALA R  72 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ASN R  81 " --> pdb=" O   GLY R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 101 through 118
    Processing helix  chain 'R' and resid 119 through 124
      removed outlier: 3.863A  pdb=" N   GLU R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU R 124 " --> pdb=" O   MET R 120 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 119 through 124'
    Processing helix  chain 'R' and resid 137 through 172
    Processing helix  chain 'R' and resid 172 through 180
      removed outlier: 3.831A  pdb=" N   THR R 178 " --> pdb=" O   PHE R 174 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 181 through 193
    Processing helix  chain 'R' and resid 196 through 201
      removed outlier: 3.562A  pdb=" N   ALA R 200 " --> pdb=" O   SER R 196 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 201 through 206
      removed outlier: 3.505A  pdb=" N   THR R 206 " --> pdb=" O   PRO R 202 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 218 through 222
    Processing helix  chain 'R' and resid 229 through 245
    Processing helix  chain 'R' and resid 245 through 271
    Processing helix  chain 'R' and resid 292 through 328
      removed outlier: 3.861A  pdb=" N   VAL R 309 " --> pdb=" O   LEU R 305 " (cutoff:3.500A)
      Proline residue:  R 318  - end of helix
      removed outlier: 3.854A  pdb=" N   CYS R 327 " --> pdb=" O   ARG R 323 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 335 through 368
      removed outlier: 3.612A  pdb=" N   SER R 357 " --> pdb=" O   PHE R 353 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   ASN R 360 " --> pdb=" O   SER R 356 " (cutoff:3.500A)
      Proline residue:  R 361  - end of helix
      removed outlier: 3.629A  pdb=" N   SER R 368 " --> pdb=" O   TYR R 364 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 368 through 378
      removed outlier: 3.792A  pdb=" N   ILE R 374 " --> pdb=" O   ASN R 370 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 3 through 19
    Processing helix  chain 'G' and resid 23 through 28
      removed outlier: 3.632A  pdb=" N   ALA G  28 " --> pdb=" O   ALA G  25 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 36 through 38
      No H-bonds generated for 'chain 'G' and resid 36 through 38'
    Processing helix  chain 'G' and resid 39 through 49
      removed outlier: 4.175A  pdb=" N   LYS G  45 " --> pdb=" O   SER G  41 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 54 through 60
    Processing helix  chain 'G' and resid 61 through 76
      removed outlier: 3.763A  pdb=" N   LEU G  76 " --> pdb=" O   CYS G  72 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 94
      removed outlier: 3.687A  pdb=" N   LYS G  94 " --> pdb=" O   LYS G  90 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 97 through 113
      removed outlier: 4.147A  pdb=" N   VAL G 103 " --> pdb=" O   GLU G  99 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 113 through 119
    Processing helix  chain 'G' and resid 125 through 138
      removed outlier: 3.700A  pdb=" N   LYS G 138 " --> pdb=" O   GLY G 134 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 146 through 158
    Processing helix  chain 'G' and resid 159 through 168
      removed outlier: 3.509A  pdb=" N   GLN G 163 " --> pdb=" O   GLY G 159 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 169 through 183
    Processing helix  chain 'G' and resid 187 through 189
      No H-bonds generated for 'chain 'G' and resid 187 through 189'
    Processing helix  chain 'G' and resid 224 through 230
    Processing helix  chain 'G' and resid 232 through 248
      removed outlier: 3.779A  pdb=" N   THR G 248 " --> pdb=" O   SER G 244 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 278 through 287
      removed outlier: 3.517A  pdb=" N   HIS G 282 " --> pdb=" O   ASP G 278 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 290 through 311
      removed outlier: 4.155A  pdb=" N   PHE G 296 " --> pdb=" O   PRO G 292 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   TYR G 297 " --> pdb=" O   ASP G 293 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ARG G 311 " --> pdb=" O   HIS G 307 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 319 through 321
      No H-bonds generated for 'chain 'G' and resid 319 through 321'
    Processing helix  chain 'G' and resid 358 through 363
    Processing helix  chain 'G' and resid 370 through 387
      removed outlier: 3.980A  pdb=" N   TRP G 374 " --> pdb=" O   SER G 370 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   PHE G 375 " --> pdb=" O   SER G 371 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 398 through 403
    Processing helix  chain 'G' and resid 404 through 408
      removed outlier: 3.911A  pdb=" N   THR G 408 " --> pdb=" O   MET G 405 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 418 through 429
    Processing helix  chain 'G' and resid 443 through 449
      removed outlier: 3.723A  pdb=" N   VAL G 447 " --> pdb=" O   GLY G 443 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 450 through 454
    Processing helix  chain 'G' and resid 457 through 464
    Processing helix  chain 'G' and resid 481 through 486
    Processing helix  chain 'G' and resid 489 through 494
    Processing helix  chain 'G' and resid 499 through 504
    Processing helix  chain 'G' and resid 505 through 507
      No H-bonds generated for 'chain 'G' and resid 505 through 507'
    Processing helix  chain 'G' and resid 513 through 525
    Processing helix  chain 'G' and resid 525 through 548
    Processing helix  chain 'G' and resid 636 through 659
    Processing helix  chain 'Q' and resid 51 through 64
    Processing helix  chain 'Q' and resid 68 through 98
      removed outlier: 4.053A  pdb=" N   LYS Q  77 " --> pdb=" O   ARG Q  73 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU Q  78 " --> pdb=" O   GLY Q  74 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 103 through 116
      removed outlier: 3.563A  pdb=" N   LYS Q 107 " --> pdb=" O   TYR Q 103 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ALA Q 108 " --> pdb=" O   GLU Q 104 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   HIS Q 109 " --> pdb=" O   HIS Q 105 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 125 through 138
      removed outlier: 3.790A  pdb=" N   ASP Q 130 " --> pdb=" O   ASN Q 126 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ALA Q 131 " --> pdb=" O   PRO Q 127 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 138 through 147
    Processing helix  chain 'Q' and resid 148 through 151
    Processing helix  chain 'Q' and resid 156 through 164
    Processing helix  chain 'Q' and resid 164 through 169
    Processing helix  chain 'Q' and resid 175 through 181
    Processing helix  chain 'Q' and resid 209 through 214
      removed outlier: 4.243A  pdb=" N   ARG Q 214 " --> pdb=" O   ARG Q 210 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 215 through 220
      removed outlier: 3.875A  pdb=" N   HIS Q 218 " --> pdb=" O   LYS Q 215 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   PHE Q 220 " --> pdb=" O   ILE Q 217 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 233 through 236
      removed outlier: 3.602A  pdb=" N   ASP Q 236 " --> pdb=" O   SER Q 233 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'Q' and resid 233 through 236'
    Processing helix  chain 'Q' and resid 246 through 261
    Processing helix  chain 'Q' and resid 262 through 265
    Processing helix  chain 'Q' and resid 275 through 286
      removed outlier: 4.073A  pdb=" N   GLU Q 281 " --> pdb=" O   ASP Q 277 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   MET Q 284 " --> pdb=" O   GLU Q 280 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 287 through 292
      removed outlier: 4.122A  pdb=" N   TYR Q 291 " --> pdb=" O   HIS Q 287 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 301 through 316
      removed outlier: 3.791A  pdb=" N   LEU Q 316 " --> pdb=" O   MET Q 312 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 333 through 352
      removed outlier: 3.651A  pdb=" N   ALA Q 343 " --> pdb=" O   PHE Q 339 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ASP Q 346 " --> pdb=" O   ALA Q 342 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'G' and resid 191 through 200
      removed outlier: 4.646A  pdb=" N   GLY G 207 " --> pdb=" O   HIS G 194 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   ILE G 196 " --> pdb=" O   VAL G 205 " (cutoff:3.500A)
      removed outlier: 7.381A  pdb=" N   VAL G 205 " --> pdb=" O   ILE G 196 " (cutoff:3.500A)
      removed outlier: 7.628A  pdb=" N   GLY G 198 " --> pdb=" O   GLY G 203 " (cutoff:3.500A)
      removed outlier: 7.782A  pdb=" N   GLY G 203 " --> pdb=" O   GLY G 198 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   TYR G 259 " --> pdb=" O   ILE G 270 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   ASP G 272 " --> pdb=" O   MET G 257 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   MET G 257 " --> pdb=" O   ASP G 272 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'G' and resid 313 through 314
    Processing sheet with id=AA3, first strand: chain 'G' and resid 323 through 325
    Processing sheet with id=AA4, first strand: chain 'G' and resid 597 through 602
      removed outlier: 4.741A  pdb=" N   SER G 599 " --> pdb=" O   TRP G 590 " (cutoff:3.500A)
      removed outlier: 5.554A  pdb=" N   TRP G 590 " --> pdb=" O   SER G 599 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   TYR G 582 " --> pdb=" O   GLU G 589 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   TYR G 580 " --> pdb=" O   ARG G 591 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   MET G 561 " --> pdb=" O   LEU G 583 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'Q' and resid 190 through 192
      removed outlier: 5.954A  pdb=" N   LEU Q  40 " --> pdb=" O   ARG Q 202 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   VAL Q 204 " --> pdb=" O   LEU Q  40 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   LEU Q  42 " --> pdb=" O   VAL Q 204 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   LYS Q  41 " --> pdb=" O   SER Q 225 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   MET Q 227 " --> pdb=" O   LYS Q  41 " (cutoff:3.500A)
      removed outlier: 5.918A  pdb=" N   LEU Q  43 " --> pdb=" O   MET Q 227 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   LEU Q 229 " --> pdb=" O   LEU Q  43 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   LEU Q  45 " --> pdb=" O   LEU Q 229 " (cutoff:3.500A)
      removed outlier: 8.255A  pdb=" N   ALA Q 231 " --> pdb=" O   LEU Q  45 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   SER Q 268 " --> pdb=" O   THR Q 224 " (cutoff:3.500A)

    576 hydrogen bonds defined for protein.
    1674 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.47

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1556
        1.29 -     1.42: 2551
        1.42 -     1.55: 5597
        1.55 -     1.68: 9
        1.68 -     1.81: 91
  Bond restraints: 9804
  Sorted by residual:
  bond pdb=" C13 SRW R 501 "
       pdb=" C16 SRW R 501 "
    ideal  model  delta    sigma   weight residual
    1.447  1.284  0.163 2.00e-02 2.50e+03 6.60e+01
  bond pdb=" C14 SRW R 501 "
       pdb=" N3  SRW R 501 "
    ideal  model  delta    sigma   weight residual
    1.309  1.453 -0.144 2.00e-02 2.50e+03 5.17e+01
  bond pdb=" C13 SRW R 501 "
       pdb=" N1  SRW R 501 "
    ideal  model  delta    sigma   weight residual
    1.357  1.487 -0.130 2.00e-02 2.50e+03 4.20e+01
  bond pdb=" C   ASP G 637 "
       pdb=" O   ASP G 637 "
    ideal  model  delta    sigma   weight residual
    1.243  1.179  0.064 9.90e-03 1.02e+04 4.13e+01
  bond pdb=" C   ILE G 529 "
       pdb=" O   ILE G 529 "
    ideal  model  delta    sigma   weight residual
    1.237  1.166  0.070 1.13e-02 7.83e+03 3.89e+01
  ... (remaining 9799 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.26: 13357
       14.26 -    28.52: 4
       28.52 -    42.78: 0
       42.78 -    57.04: 0
       57.04 -    71.30: 2
  Bond angle restraints: 13363
  Sorted by residual:
  angle pdb=" F1  ALF Q 403 "
        pdb="AL   ALF Q 403 "
        pdb=" F2  ALF Q 403 "
      ideal   model   delta    sigma   weight residual
     108.68  179.98  -71.30 3.00e+00 1.11e-01 5.65e+02
  angle pdb=" F3  ALF Q 403 "
        pdb="AL   ALF Q 403 "
        pdb=" F4  ALF Q 403 "
      ideal   model   delta    sigma   weight residual
     109.63  179.96  -70.33 3.00e+00 1.11e-01 5.50e+02
  angle pdb=" F2  ALF Q 403 "
        pdb="AL   ALF Q 403 "
        pdb=" F4  ALF Q 403 "
      ideal   model   delta    sigma   weight residual
     110.21   90.01   20.20 3.00e+00 1.11e-01 4.53e+01
  angle pdb=" F1  ALF Q 403 "
        pdb="AL   ALF Q 403 "
        pdb=" F3  ALF Q 403 "
      ideal   model   delta    sigma   weight residual
     109.69   90.03   19.66 3.00e+00 1.11e-01 4.30e+01
  angle pdb=" F2  ALF Q 403 "
        pdb="AL   ALF Q 403 "
        pdb=" F3  ALF Q 403 "
      ideal   model   delta    sigma   weight residual
     109.59   89.98   19.61 3.00e+00 1.11e-01 4.27e+01
  ... (remaining 13358 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.65: 5607
       30.65 -    61.31: 193
       61.31 -    91.96: 23
       91.96 -   122.62: 4
      122.62 -   153.27: 3
  Dihedral angle restraints: 5830
    sinusoidal: 2080
      harmonic: 3750
  Sorted by residual:
  dihedral pdb=" CB  CYS R 141 "
           pdb=" SG  CYS R 141 "
           pdb=" SG  CYS R 224 "
           pdb=" CB  CYS R 224 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -137.78   51.78     1      1.00e+01 1.00e-02 3.66e+01
  dihedral pdb=" O2B GDP Q 401 "
           pdb=" O3A GDP Q 401 "
           pdb=" PB  GDP Q 401 "
           pdb=" PA  GDP Q 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00   66.50  113.50     1      2.00e+01 2.50e-03 3.36e+01
  dihedral pdb=" C25 SRW R 501 "
           pdb=" C24 SRW R 501 "
           pdb=" C26 SRW R 501 "
           pdb=" F1  SRW R 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     106.02 -100.71 -153.27     1      3.00e+01 1.11e-03 2.02e+01
  ... (remaining 5827 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1421
       0.073 -    0.147: 117
       0.147 -    0.220: 1
       0.220 -    0.293: 0
       0.293 -    0.367: 2
  Chirality restraints: 1541
  Sorted by residual:
  chirality pdb=" C24 SRW R 501 "
            pdb=" C14 SRW R 501 "
            pdb=" C25 SRW R 501 "
            pdb=" F1  SRW R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       1.45    1.82   -0.37 2.00e-01 2.50e+01 3.36e+00
  chirality pdb=" CG  LEU R 105 "
            pdb=" CB  LEU R 105 "
            pdb=" CD1 LEU R 105 "
            pdb=" CD2 LEU R 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.27   -0.32 2.00e-01 2.50e+01 2.59e+00
  chirality pdb=" C8  SRW R 501 "
            pdb=" C12 SRW R 501 "
            pdb=" C3  SRW R 501 "
            pdb=" C9  SRW R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.46   -2.64    0.18 2.00e-01 2.50e+01 8.09e-01
  ... (remaining 1538 not shown)

  Planarity restraints: 1697
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP G 590 "    0.018 2.00e-02 2.50e+03   3.53e-02 1.24e+01
        pdb=" C   TRP G 590 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   TRP G 590 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ARG G 591 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP G 635 "    0.017 2.00e-02 2.50e+03   3.43e-02 1.18e+01
        pdb=" C   ASP G 635 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   ASP G 635 "    0.023 2.00e-02 2.50e+03
        pdb=" N   SER G 636 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G 637 "   -0.044 5.00e-02 4.00e+02   6.75e-02 7.29e+00
        pdb=" N   PRO G 638 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO G 638 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO G 638 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1694 not shown)

  Histogram of nonbonded interaction distances:
        1.86 -     2.47: 33
        2.47 -     3.08: 7053
        3.08 -     3.69: 14653
        3.69 -     4.29: 21118
        4.29 -     4.90: 35477
  Nonbonded interactions: 78334
  Sorted by model distance:
  nonbonded pdb=" O3B GDP Q 401 "
            pdb="MG    MG Q 402 "
     model   vdw
     1.865 2.170
  nonbonded pdb=" OG  SER Q  53 "
            pdb="MG    MG Q 402 "
     model   vdw
     1.898 2.170
  nonbonded pdb=" O   PHE R 345 "
            pdb=" OG1 THR R 349 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" O   THR G 406 "
            pdb=" NH2 ARG G 431 "
     model   vdw
     2.282 3.120
  nonbonded pdb=" O   LYS Q  77 "
            pdb=" OE1 GLN Q  81 "
     model   vdw
     2.285 3.040
  ... (remaining 78329 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     10.060
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
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   0.263   9806  Z= 0.382
  Angle     :  1.166  71.296  13365  Z= 0.483
  Chirality :  0.040   0.367   1541
  Planarity :  0.004   0.067   1697
  Dihedral  : 15.900 153.273   3393
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  : 12.71 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.24), residues: 1266
  helix:  1.47 (0.20), residues: 691
  sheet:  0.11 (0.51), residues: 107
  loop : -0.42 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG G 516 
 TYR   0.025   0.001   TYR G 651 
 PHE   0.016   0.001   PHE G 296 
 TRP   0.026   0.001   TRP G 590 
 HIS   0.009   0.001   HIS G 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 ( 9804)
  covalent geometry    : angle       1.14843 (13363)
  SS BOND              : bond        0.26303 (    1)
  SS BOND              : angle      16.39518 (    2)
  hydrogen bonds       : bond        0.13488 (  576)
  hydrogen bonds       : angle       6.05956 ( 1674)
  Misc. bond           : bond        0.18638 (    1)

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 223
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  144 TYR cc_start: 0.6057 (t80) cc_final: 0.5704 (t80)
REVERT: Q   94 MET cc_start: 0.7325 (mmm) cc_final: 0.6853 (mtp)
REVERT: Q  256 ARG cc_start: 0.7845 (tpt170) cc_final: 0.7588 (ttt-90)
REVERT: Q  277 ASP cc_start: 0.7646 (p0) cc_final: 0.7347 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 224
  average time/residue: 0.1044
  time to fit residues: 32.2357
Evaluate side-chains
  164 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:   10.0000
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 123 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
R 104 HIS
** R 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 577 GLN
** Q  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.167521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.118413 restraints weight = 14503.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 2.70
r_work: 0.3202 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9806  Z= 0.216
  Angle     :  0.854  30.312  13365  Z= 0.376
  Chirality :  0.044   0.195   1541
  Planarity :  0.004   0.043   1697
  Dihedral  : 11.605 148.283   1421
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 14.59 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.24), residues: 1266
  helix:  1.33 (0.19), residues: 720
  sheet:  0.29 (0.49), residues: 110
  loop : -0.49 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG Q  92 
 TYR   0.027   0.002   TYR R 364 
 PHE   0.017   0.002   PHE Q 328 
 TRP   0.019   0.002   TRP G 590 
 HIS   0.009   0.001   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 ( 9804)
  covalent geometry    : angle       0.85368 (13363)
  SS BOND              : bond        0.00158 (    1)
  SS BOND              : angle       1.23144 (    2)
  hydrogen bonds       : bond        0.04425 (  576)
  hydrogen bonds       : angle       4.98271 ( 1674)
  Misc. bond           : bond        0.00196 (    1)

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 180
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  148 ARG cc_start: 0.7388 (ttm110) cc_final: 0.6391 (mpt-90)
REVERT: R  149 ASP cc_start: 0.5558 (t0) cc_final: 0.5337 (t0)
REVERT: R  354 TYR cc_start: 0.8306 (m-80) cc_final: 0.8011 (m-80)
REVERT: G  537 GLU cc_start: 0.7934 (mp0) cc_final: 0.7481 (mp0)
REVERT: Q   94 MET cc_start: 0.7840 (mmm) cc_final: 0.7510 (mtp)
REVERT: Q  256 ARG cc_start: 0.8478 (tpt170) cc_final: 0.7970 (ttt-90)
  outliers start: 26
  outliers final: 16
  residues processed: 201
  average time/residue: 0.1021
  time to fit residues: 28.8142
Evaluate side-chains
  178 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 162
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   53 GLU
Chi-restraints excluded: chain R residue   57 ASN
Chi-restraints excluded: chain R residue  151 CYS
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  300 HIS
Chi-restraints excluded: chain R residue  309 VAL
Chi-restraints excluded: chain R residue  359 ILE
Chi-restraints excluded: chain R residue  367 VAL
Chi-restraints excluded: chain G residue  295 ILE
Chi-restraints excluded: chain G residue  351 VAL
Chi-restraints excluded: chain G residue  463 LEU
Chi-restraints excluded: chain G residue  505 LEU
Chi-restraints excluded: chain G residue  598 GLN
Chi-restraints excluded: chain G residue  636 SER
Chi-restraints excluded: chain G residue  651 TYR
Chi-restraints excluded: chain Q residue  270 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 120 optimal weight:   40.0000
   chunk 116 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   chunk 100 optimal weight:    6.9990
   chunk 19 optimal weight:    0.7980
   chunk 117 optimal weight:    0.6980
   chunk 98 optimal weight:    6.9990
   chunk 70 optimal weight:    9.9990
   chunk 34 optimal weight:    0.5980
   chunk 22 optimal weight:    9.9990
   overall best weight:    1.9982

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

Flipped N/Q/H residues before XYZ refinement:
R 104 HIS
Q  82 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.166278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.117395 restraints weight = 14356.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 2.68
r_work: 0.3180 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9806  Z= 0.225
  Angle     :  0.847  29.959  13365  Z= 0.369
  Chirality :  0.044   0.232   1541
  Planarity :  0.004   0.046   1697
  Dihedral  : 11.316 148.507   1421
  Min Nonbonded Distance : 1.750

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 16.35 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.24), residues: 1266
  helix:  1.27 (0.19), residues: 707
  sheet:  0.15 (0.47), residues: 110
  loop : -0.38 (0.31), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG Q  92 
 TYR   0.033   0.002   TYR R 364 
 PHE   0.038   0.002   PHE R 188 
 TRP   0.018   0.002   TRP G 590 
 HIS   0.007   0.001   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 ( 9804)
  covalent geometry    : angle       0.84663 (13363)
  SS BOND              : bond        0.00170 (    1)
  SS BOND              : angle       0.62471 (    2)
  hydrogen bonds       : bond        0.04151 (  576)
  hydrogen bonds       : angle       4.82959 ( 1674)
  Misc. bond           : bond        0.00098 (    1)

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 176
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  148 ARG cc_start: 0.7215 (ttm110) cc_final: 0.6907 (tpp80)
REVERT: G  405 MET cc_start: 0.7793 (ppp) cc_final: 0.7254 (ppp)
REVERT: Q   49 GLU cc_start: 0.8520 (tp30) cc_final: 0.7718 (mt-10)
REVERT: Q   94 MET cc_start: 0.7867 (mmm) cc_final: 0.7626 (mtp)
REVERT: Q  183 ARG cc_start: 0.8599 (tpt-90) cc_final: 0.8320 (tpt-90)
REVERT: Q  256 ARG cc_start: 0.8416 (tpt170) cc_final: 0.7771 (ttt-90)
REVERT: Q  280 GLU cc_start: 0.8958 (pt0) cc_final: 0.8716 (pt0)
  outliers start: 27
  outliers final: 17
  residues processed: 194
  average time/residue: 0.1059
  time to fit residues: 28.1155
Evaluate side-chains
  178 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 161
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   53 GLU
Chi-restraints excluded: chain R residue   57 ASN
Chi-restraints excluded: chain R residue  151 CYS
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  300 HIS
Chi-restraints excluded: chain R residue  309 VAL
Chi-restraints excluded: chain R residue  324 LEU
Chi-restraints excluded: chain R residue  359 ILE
Chi-restraints excluded: chain R residue  367 VAL
Chi-restraints excluded: chain G residue  295 ILE
Chi-restraints excluded: chain G residue  344 LYS
Chi-restraints excluded: chain G residue  351 VAL
Chi-restraints excluded: chain G residue  505 LEU
Chi-restraints excluded: chain G residue  636 SER
Chi-restraints excluded: chain G residue  651 TYR
Chi-restraints excluded: chain Q residue  192 TYR
Chi-restraints excluded: chain Q residue  270 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 116 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 67 optimal weight:    0.5980
   chunk 115 optimal weight:    4.9990
   chunk 98 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    0.8980
   chunk 83 optimal weight:    3.9990
   chunk 95 optimal weight:    0.7980
   chunk 79 optimal weight:    0.7980
   chunk 118 optimal weight:    6.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
R 104 HIS
R 261 ASN
** Q  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  82 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.167435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.120019 restraints weight = 14440.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 2.73
r_work: 0.3207 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.2478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9806  Z= 0.148
  Angle     :  0.809  30.191  13365  Z= 0.345
  Chirality :  0.042   0.234   1541
  Planarity :  0.004   0.046   1697
  Dihedral  : 10.801 148.312   1421
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 18.23 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.24), residues: 1266
  helix:  1.49 (0.19), residues: 708
  sheet:  0.14 (0.47), residues: 110
  loop : -0.44 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG Q  92 
 TYR   0.025   0.001   TYR R 364 
 PHE   0.042   0.001   PHE R 188 
 TRP   0.008   0.001   TRP G 590 
 HIS   0.009   0.001   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9804)
  covalent geometry    : angle       0.80913 (13363)
  SS BOND              : bond        0.00106 (    1)
  SS BOND              : angle       0.43915 (    2)
  hydrogen bonds       : bond        0.03711 (  576)
  hydrogen bonds       : angle       4.64975 ( 1674)
  Misc. bond           : bond        0.00094 (    1)

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 182
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  148 ARG cc_start: 0.7165 (ttm110) cc_final: 0.6878 (tpp80)
REVERT: R  240 ASN cc_start: 0.6228 (t0) cc_final: 0.5783 (m110)
REVERT: R  243 MET cc_start: 0.5383 (tmm) cc_final: 0.5065 (ppp)
REVERT: R  261 ASN cc_start: 0.8014 (m-40) cc_final: 0.7634 (m110)
REVERT: R  322 ARG cc_start: 0.6533 (tmm-80) cc_final: 0.6304 (tmm-80)
REVERT: R  354 TYR cc_start: 0.8251 (m-80) cc_final: 0.8013 (m-80)
REVERT: G  405 MET cc_start: 0.7894 (ppp) cc_final: 0.7317 (ppp)
REVERT: G  431 ARG cc_start: 0.8174 (mmm-85) cc_final: 0.7601 (mtm180)
REVERT: Q   49 GLU cc_start: 0.8516 (tp30) cc_final: 0.7691 (mt-10)
REVERT: Q   94 MET cc_start: 0.7829 (mmm) cc_final: 0.7469 (mtp)
REVERT: Q  183 ARG cc_start: 0.8700 (tpt-90) cc_final: 0.8426 (tpt-90)
REVERT: Q  256 ARG cc_start: 0.8462 (tpt170) cc_final: 0.7817 (ttt-90)
REVERT: Q  276 LYS cc_start: 0.8332 (pttt) cc_final: 0.8026 (pttm)
REVERT: Q  280 GLU cc_start: 0.8941 (pt0) cc_final: 0.8716 (pt0)
  outliers start: 22
  outliers final: 17
  residues processed: 195
  average time/residue: 0.1136
  time to fit residues: 30.0229
Evaluate side-chains
  183 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   53 GLU
Chi-restraints excluded: chain R residue   57 ASN
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  300 HIS
Chi-restraints excluded: chain R residue  309 VAL
Chi-restraints excluded: chain R residue  324 LEU
Chi-restraints excluded: chain R residue  359 ILE
Chi-restraints excluded: chain R residue  367 VAL
Chi-restraints excluded: chain G residue  295 ILE
Chi-restraints excluded: chain G residue  344 LYS
Chi-restraints excluded: chain G residue  351 VAL
Chi-restraints excluded: chain G residue  505 LEU
Chi-restraints excluded: chain G residue  636 SER
Chi-restraints excluded: chain G residue  651 TYR
Chi-restraints excluded: chain Q residue  192 TYR
Chi-restraints excluded: chain Q residue  203 MET
Chi-restraints excluded: chain Q residue  270 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 77 optimal weight:    0.0470
   chunk 81 optimal weight:    0.7980
   chunk 78 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 80 optimal weight:    0.3980
   chunk 70 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 110 optimal weight:    0.0170
   overall best weight:    0.4316

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

Flipped N/Q/H residues before XYZ refinement:
R 104 HIS
R 269 GLN
G 135 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.169643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.123232 restraints weight = 14401.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 2.69
r_work: 0.3244 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.2684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9806  Z= 0.112
  Angle     :  0.791  30.213  13365  Z= 0.333
  Chirality :  0.041   0.232   1541
  Planarity :  0.004   0.046   1697
  Dihedral  : 10.390 148.140   1421
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.45 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.24), residues: 1266
  helix:  1.63 (0.19), residues: 708
  sheet:  0.09 (0.46), residues: 117
  loop : -0.38 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG Q  92 
 TYR   0.024   0.001   TYR R 364 
 PHE   0.043   0.001   PHE R 188 
 TRP   0.009   0.001   TRP R 193 
 HIS   0.008   0.001   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 9804)
  covalent geometry    : angle       0.79130 (13363)
  SS BOND              : bond        0.00047 (    1)
  SS BOND              : angle       0.49046 (    2)
  hydrogen bonds       : bond        0.03430 (  576)
  hydrogen bonds       : angle       4.49480 ( 1674)
  Misc. bond           : bond        0.00056 (    1)

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 183
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  148 ARG cc_start: 0.7186 (ttm110) cc_final: 0.6873 (tpp80)
REVERT: R  240 ASN cc_start: 0.6314 (t0) cc_final: 0.5721 (m110)
REVERT: R  243 MET cc_start: 0.5178 (tmm) cc_final: 0.4974 (ppp)
REVERT: R  261 ASN cc_start: 0.8120 (m-40) cc_final: 0.7781 (m110)
REVERT: R  269 GLN cc_start: 0.6669 (mm110) cc_final: 0.6170 (pt0)
REVERT: G  405 MET cc_start: 0.7735 (ppp) cc_final: 0.7245 (ppp)
REVERT: G  431 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.7512 (mtm180)
REVERT: G  537 GLU cc_start: 0.7985 (mp0) cc_final: 0.7686 (mp0)
REVERT: G  568 MET cc_start: 0.7039 (tpt) cc_final: 0.5975 (tpt)
REVERT: Q   49 GLU cc_start: 0.8502 (tp30) cc_final: 0.7685 (mt-10)
REVERT: Q   82 ASN cc_start: 0.8168 (t0) cc_final: 0.7862 (t0)
REVERT: Q   94 MET cc_start: 0.7779 (mmm) cc_final: 0.7373 (mtp)
REVERT: Q  256 ARG cc_start: 0.8452 (tpt170) cc_final: 0.7842 (ttt-90)
REVERT: Q  280 GLU cc_start: 0.8932 (pt0) cc_final: 0.8720 (pt0)
  outliers start: 23
  outliers final: 13
  residues processed: 200
  average time/residue: 0.1058
  time to fit residues: 29.0659
Evaluate side-chains
  175 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 162
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   53 GLU
Chi-restraints excluded: chain R residue   57 ASN
Chi-restraints excluded: chain R residue  151 CYS
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  300 HIS
Chi-restraints excluded: chain R residue  309 VAL
Chi-restraints excluded: chain R residue  359 ILE
Chi-restraints excluded: chain R residue  367 VAL
Chi-restraints excluded: chain G residue  505 LEU
Chi-restraints excluded: chain G residue  636 SER
Chi-restraints excluded: chain G residue  651 TYR
Chi-restraints excluded: chain Q residue   56 ILE
Chi-restraints excluded: chain Q residue  270 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 116 optimal weight:    0.0170
   chunk 34 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 80 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 26 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   chunk 9 optimal weight:    9.9990
   chunk 113 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.7418

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

Flipped N/Q/H residues before XYZ refinement:
R 240 ASN
G 135 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.169200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.121841 restraints weight = 14385.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.59
r_work: 0.3241 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3097 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9806  Z= 0.125
  Angle     :  0.793  30.406  13365  Z= 0.333
  Chirality :  0.041   0.218   1541
  Planarity :  0.004   0.046   1697
  Dihedral  : 10.336 148.291   1421
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 18.90 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.24), residues: 1266
  helix:  1.74 (0.20), residues: 708
  sheet:  0.30 (0.48), residues: 109
  loop : -0.34 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG Q  92 
 TYR   0.022   0.001   TYR Q 159 
 PHE   0.046   0.001   PHE R 188 
 TRP   0.009   0.001   TRP G 458 
 HIS   0.005   0.001   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9804)
  covalent geometry    : angle       0.79301 (13363)
  SS BOND              : bond        0.00088 (    1)
  SS BOND              : angle       0.41846 (    2)
  hydrogen bonds       : bond        0.03423 (  576)
  hydrogen bonds       : angle       4.43295 ( 1674)
  Misc. bond           : bond        0.00070 (    1)

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 170
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  322 ARG cc_start: 0.6569 (tmm-80) cc_final: 0.6342 (tmm-80)
REVERT: G  405 MET cc_start: 0.7738 (ppp) cc_final: 0.7154 (ppp)
REVERT: G  568 MET cc_start: 0.7024 (tpt) cc_final: 0.5983 (tpt)
REVERT: Q   49 GLU cc_start: 0.8513 (tp30) cc_final: 0.7698 (mt-10)
REVERT: Q   82 ASN cc_start: 0.8136 (t0) cc_final: 0.7880 (t0)
REVERT: Q   94 MET cc_start: 0.7771 (mmm) cc_final: 0.7385 (mtp)
REVERT: Q  248 MET cc_start: 0.8826 (ttm) cc_final: 0.8520 (mtm)
REVERT: Q  256 ARG cc_start: 0.8496 (tpt170) cc_final: 0.7903 (ttt-90)
REVERT: Q  280 GLU cc_start: 0.8935 (pt0) cc_final: 0.8718 (pt0)
  outliers start: 24
  outliers final: 18
  residues processed: 186
  average time/residue: 0.1123
  time to fit residues: 28.6113
Evaluate side-chains
  184 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 166
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   53 GLU
Chi-restraints excluded: chain R residue   57 ASN
Chi-restraints excluded: chain R residue  151 CYS
Chi-restraints excluded: chain R residue  172 HIS
Chi-restraints excluded: chain R residue  240 ASN
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  300 HIS
Chi-restraints excluded: chain R residue  309 VAL
Chi-restraints excluded: chain R residue  324 LEU
Chi-restraints excluded: chain R residue  359 ILE
Chi-restraints excluded: chain R residue  367 VAL
Chi-restraints excluded: chain G residue  295 ILE
Chi-restraints excluded: chain G residue  413 LEU
Chi-restraints excluded: chain G residue  505 LEU
Chi-restraints excluded: chain G residue  511 LEU
Chi-restraints excluded: chain G residue  636 SER
Chi-restraints excluded: chain G residue  651 TYR
Chi-restraints excluded: chain Q residue  270 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 85 optimal weight:    8.9990
   chunk 107 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9980
   chunk 121 optimal weight:    8.9990
   chunk 68 optimal weight:    0.9980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
R 240 ASN
G 135 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.168331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.120704 restraints weight = 14469.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.61
r_work: 0.3227 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.2968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9806  Z= 0.150
  Angle     :  0.815  30.627  13365  Z= 0.343
  Chirality :  0.042   0.215   1541
  Planarity :  0.004   0.051   1697
  Dihedral  : 10.311 148.297   1421
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 18.90 %
    Favored  : 77.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.24), residues: 1266
  helix:  1.77 (0.20), residues: 708
  sheet:  0.26 (0.48), residues: 110
  loop : -0.34 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG Q  92 
 TYR   0.023   0.001   TYR R 364 
 PHE   0.046   0.001   PHE R 188 
 TRP   0.009   0.001   TRP G 458 
 HIS   0.005   0.001   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 9804)
  covalent geometry    : angle       0.81538 (13363)
  SS BOND              : bond        0.00074 (    1)
  SS BOND              : angle       0.44731 (    2)
  hydrogen bonds       : bond        0.03518 (  576)
  hydrogen bonds       : angle       4.45172 ( 1674)
  Misc. bond           : bond        0.00059 (    1)

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 169
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  148 ARG cc_start: 0.7228 (ttm110) cc_final: 0.6853 (tpp80)
REVERT: R  243 MET cc_start: 0.5385 (tmm) cc_final: 0.5056 (ppp)
REVERT: G  189 ASN cc_start: 0.8762 (t0) cc_final: 0.8407 (t0)
REVERT: G  405 MET cc_start: 0.7780 (ppp) cc_final: 0.7077 (ppp)
REVERT: G  431 ARG cc_start: 0.8067 (mmm-85) cc_final: 0.7139 (mtt180)
REVERT: G  537 GLU cc_start: 0.7780 (mp0) cc_final: 0.7537 (mp0)
REVERT: G  568 MET cc_start: 0.7112 (tpt) cc_final: 0.6052 (tpt)
REVERT: Q   49 GLU cc_start: 0.8529 (tp30) cc_final: 0.7700 (mt-10)
REVERT: Q   82 ASN cc_start: 0.8139 (t0) cc_final: 0.7869 (t0)
REVERT: Q   94 MET cc_start: 0.7783 (mmm) cc_final: 0.7394 (mtp)
REVERT: Q  190 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7818 (pt)
REVERT: Q  256 ARG cc_start: 0.8496 (tpt170) cc_final: 0.7887 (ttt-90)
REVERT: Q  280 GLU cc_start: 0.8934 (pt0) cc_final: 0.8708 (pt0)
  outliers start: 29
  outliers final: 20
  residues processed: 190
  average time/residue: 0.1070
  time to fit residues: 28.0224
Evaluate side-chains
  182 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 161
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   12 ILE
Chi-restraints excluded: chain R residue   53 GLU
Chi-restraints excluded: chain R residue   57 ASN
Chi-restraints excluded: chain R residue  151 CYS
Chi-restraints excluded: chain R residue  172 HIS
Chi-restraints excluded: chain R residue  240 ASN
Chi-restraints excluded: chain R residue  300 HIS
Chi-restraints excluded: chain R residue  309 VAL
Chi-restraints excluded: chain R residue  324 LEU
Chi-restraints excluded: chain R residue  359 ILE
Chi-restraints excluded: chain R residue  367 VAL
Chi-restraints excluded: chain G residue  295 ILE
Chi-restraints excluded: chain G residue  314 VAL
Chi-restraints excluded: chain G residue  413 LEU
Chi-restraints excluded: chain G residue  505 LEU
Chi-restraints excluded: chain G residue  511 LEU
Chi-restraints excluded: chain G residue  636 SER
Chi-restraints excluded: chain G residue  651 TYR
Chi-restraints excluded: chain Q residue   56 ILE
Chi-restraints excluded: chain Q residue  190 ILE
Chi-restraints excluded: chain Q residue  270 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 80 optimal weight:    0.0970
   chunk 72 optimal weight:    0.9980
   chunk 22 optimal weight:    8.9990
   chunk 100 optimal weight:    7.9990
   chunk 73 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0570
   chunk 17 optimal weight:    6.9990
   chunk 118 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.6296

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

Flipped N/Q/H residues before XYZ refinement:
R 240 ASN
Q  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.169380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.121533 restraints weight = 14304.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.72
r_work: 0.3251 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3104 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9806  Z= 0.121
  Angle     :  0.812  30.336  13365  Z= 0.340
  Chirality :  0.041   0.233   1541
  Planarity :  0.004   0.054   1697
  Dihedral  : 10.124 148.255   1421
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 20.00 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.24), residues: 1266
  helix:  1.79 (0.20), residues: 708
  sheet:  0.35 (0.47), residues: 111
  loop : -0.35 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG Q  92 
 TYR   0.022   0.001   TYR Q 159 
 PHE   0.045   0.001   PHE R 188 
 TRP   0.009   0.001   TRP G 458 
 HIS   0.005   0.001   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9804)
  covalent geometry    : angle       0.81208 (13363)
  SS BOND              : bond        0.00053 (    1)
  SS BOND              : angle       0.45596 (    2)
  hydrogen bonds       : bond        0.03460 (  576)
  hydrogen bonds       : angle       4.45091 ( 1674)
  Misc. bond           : bond        0.00034 (    1)

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 168
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  243 MET cc_start: 0.5511 (tmm) cc_final: 0.5082 (ppp)
REVERT: R  249 MET cc_start: 0.7835 (tpp) cc_final: 0.7459 (tpp)
REVERT: R  322 ARG cc_start: 0.6548 (tmm-80) cc_final: 0.6261 (tmm-80)
REVERT: G  189 ASN cc_start: 0.8728 (t0) cc_final: 0.8384 (t0)
REVERT: G  537 GLU cc_start: 0.7821 (mp0) cc_final: 0.7528 (mp0)
REVERT: G  568 MET cc_start: 0.6919 (tpt) cc_final: 0.6166 (tpt)
REVERT: Q   49 GLU cc_start: 0.8496 (tp30) cc_final: 0.7645 (mt-10)
REVERT: Q   82 ASN cc_start: 0.8136 (t0) cc_final: 0.7911 (t0)
REVERT: Q   94 MET cc_start: 0.7807 (mmm) cc_final: 0.7395 (mtp)
REVERT: Q  152 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7246 (mt0)
REVERT: Q  190 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7745 (pt)
REVERT: Q  248 MET cc_start: 0.8783 (ttm) cc_final: 0.8507 (ttm)
REVERT: Q  256 ARG cc_start: 0.8368 (tpt170) cc_final: 0.7781 (ttt-90)
  outliers start: 23
  outliers final: 19
  residues processed: 183
  average time/residue: 0.1062
  time to fit residues: 26.8141
Evaluate side-chains
  179 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 159
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   12 ILE
Chi-restraints excluded: chain R residue   53 GLU
Chi-restraints excluded: chain R residue   57 ASN
Chi-restraints excluded: chain R residue  151 CYS
Chi-restraints excluded: chain R residue  172 HIS
Chi-restraints excluded: chain R residue  300 HIS
Chi-restraints excluded: chain R residue  309 VAL
Chi-restraints excluded: chain R residue  324 LEU
Chi-restraints excluded: chain R residue  359 ILE
Chi-restraints excluded: chain R residue  367 VAL
Chi-restraints excluded: chain G residue  413 LEU
Chi-restraints excluded: chain G residue  505 LEU
Chi-restraints excluded: chain G residue  511 LEU
Chi-restraints excluded: chain G residue  624 ILE
Chi-restraints excluded: chain G residue  636 SER
Chi-restraints excluded: chain G residue  651 TYR
Chi-restraints excluded: chain Q residue   56 ILE
Chi-restraints excluded: chain Q residue  190 ILE
Chi-restraints excluded: chain Q residue  203 MET
Chi-restraints excluded: chain Q residue  270 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 93 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   chunk 0 optimal weight:    9.9990
   chunk 76 optimal weight:    2.9990
   chunk 81 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 121 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 79 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 73 optimal weight:    8.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
Q 176 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.168521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.120362 restraints weight = 14363.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 2.69
r_work: 0.3234 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3086 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.3115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9806  Z= 0.144
  Angle     :  0.821  30.803  13365  Z= 0.346
  Chirality :  0.042   0.233   1541
  Planarity :  0.004   0.049   1697
  Dihedral  : 10.013 148.200   1421
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.67 %
    Favored  : 77.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.24), residues: 1266
  helix:  1.77 (0.20), residues: 709
  sheet:  0.44 (0.49), residues: 107
  loop : -0.37 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG Q  92 
 TYR   0.021   0.001   TYR Q 159 
 PHE   0.049   0.001   PHE R 188 
 TRP   0.020   0.001   TRP R 193 
 HIS   0.005   0.001   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 9804)
  covalent geometry    : angle       0.82139 (13363)
  SS BOND              : bond        0.00085 (    1)
  SS BOND              : angle       0.44969 (    2)
  hydrogen bonds       : bond        0.03525 (  576)
  hydrogen bonds       : angle       4.43964 ( 1674)
  Misc. bond           : bond        0.00030 (    1)

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 172
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  148 ARG cc_start: 0.6969 (ttm110) cc_final: 0.6651 (tpp80)
REVERT: R  243 MET cc_start: 0.5787 (tmm) cc_final: 0.5166 (ppp)
REVERT: R  249 MET cc_start: 0.7787 (tpp) cc_final: 0.7347 (tpt)
REVERT: R  322 ARG cc_start: 0.6511 (tmm-80) cc_final: 0.6257 (tmm-80)
REVERT: G  189 ASN cc_start: 0.8719 (t0) cc_final: 0.8375 (t0)
REVERT: G  507 ARG cc_start: 0.8368 (ttp-110) cc_final: 0.8147 (ttm110)
REVERT: G  568 MET cc_start: 0.6861 (tpt) cc_final: 0.6079 (tpt)
REVERT: Q   49 GLU cc_start: 0.8494 (tp30) cc_final: 0.7633 (mt-10)
REVERT: Q   82 ASN cc_start: 0.8133 (t0) cc_final: 0.7910 (t0)
REVERT: Q   94 MET cc_start: 0.7843 (mmm) cc_final: 0.7426 (mtp)
REVERT: Q  152 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7293 (mt0)
REVERT: Q  181 ARG cc_start: 0.7840 (mtp180) cc_final: 0.7303 (mtp85)
REVERT: Q  190 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7560 (pt)
REVERT: Q  256 ARG cc_start: 0.8297 (tpt170) cc_final: 0.7697 (ttt-90)
REVERT: Q  276 LYS cc_start: 0.8063 (pttt) cc_final: 0.7697 (pttm)
  outliers start: 22
  outliers final: 19
  residues processed: 186
  average time/residue: 0.1090
  time to fit residues: 27.7723
Evaluate side-chains
  187 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 167
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   12 ILE
Chi-restraints excluded: chain R residue   53 GLU
Chi-restraints excluded: chain R residue   57 ASN
Chi-restraints excluded: chain R residue  151 CYS
Chi-restraints excluded: chain R residue  300 HIS
Chi-restraints excluded: chain R residue  309 VAL
Chi-restraints excluded: chain R residue  359 ILE
Chi-restraints excluded: chain R residue  367 VAL
Chi-restraints excluded: chain G residue  314 VAL
Chi-restraints excluded: chain G residue  505 LEU
Chi-restraints excluded: chain G residue  511 LEU
Chi-restraints excluded: chain G residue  537 GLU
Chi-restraints excluded: chain G residue  624 ILE
Chi-restraints excluded: chain G residue  636 SER
Chi-restraints excluded: chain G residue  651 TYR
Chi-restraints excluded: chain Q residue   56 ILE
Chi-restraints excluded: chain Q residue  176 GLN
Chi-restraints excluded: chain Q residue  190 ILE
Chi-restraints excluded: chain Q residue  203 MET
Chi-restraints excluded: chain Q residue  270 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 115 optimal weight:    0.0970
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
Q  81 GLN
Q 176 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.168914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.120753 restraints weight = 14335.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 2.71
r_work: 0.3240 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9806  Z= 0.135
  Angle     :  0.818  30.590  13365  Z= 0.345
  Chirality :  0.042   0.256   1541
  Planarity :  0.004   0.059   1697
  Dihedral  :  9.835 148.145   1421
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 20.11 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.24), residues: 1266
  helix:  1.79 (0.20), residues: 709
  sheet:  0.42 (0.48), residues: 109
  loop : -0.42 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG Q  92 
 TYR   0.022   0.001   TYR Q 159 
 PHE   0.051   0.001   PHE R 188 
 TRP   0.019   0.001   TRP R 193 
 HIS   0.005   0.001   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9804)
  covalent geometry    : angle       0.81851 (13363)
  SS BOND              : bond        0.00076 (    1)
  SS BOND              : angle       0.46890 (    2)
  hydrogen bonds       : bond        0.03512 (  576)
  hydrogen bonds       : angle       4.46651 ( 1674)
  Misc. bond           : bond        0.00032 (    1)

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

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

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2532 Ramachandran restraints generated.
    1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 170
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  148 ARG cc_start: 0.7108 (ttm110) cc_final: 0.6743 (tpp80)
REVERT: R  243 MET cc_start: 0.5786 (tmm) cc_final: 0.5207 (ppp)
REVERT: R  322 ARG cc_start: 0.6583 (tmm-80) cc_final: 0.6333 (tmm-80)
REVERT: G  189 ASN cc_start: 0.8746 (t0) cc_final: 0.8421 (t0)
REVERT: G  507 ARG cc_start: 0.8418 (ttp-110) cc_final: 0.8188 (ttm110)
REVERT: Q   49 GLU cc_start: 0.8547 (tp30) cc_final: 0.7641 (mt-10)
REVERT: Q   82 ASN cc_start: 0.8131 (t0) cc_final: 0.7910 (t0)
REVERT: Q   94 MET cc_start: 0.7809 (mmm) cc_final: 0.7374 (mtp)
REVERT: Q  152 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7373 (mt0)
REVERT: Q  181 ARG cc_start: 0.7892 (mtp180) cc_final: 0.7612 (mtp85)
REVERT: Q  190 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7679 (pt)
REVERT: Q  256 ARG cc_start: 0.8384 (tpt170) cc_final: 0.7780 (ttt-90)
  outliers start: 23
  outliers final: 19
  residues processed: 185
  average time/residue: 0.1076
  time to fit residues: 27.1563
Evaluate side-chains
  184 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 164
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   12 ILE
Chi-restraints excluded: chain R residue   53 GLU
Chi-restraints excluded: chain R residue   57 ASN
Chi-restraints excluded: chain R residue  151 CYS
Chi-restraints excluded: chain R residue  172 HIS
Chi-restraints excluded: chain R residue  300 HIS
Chi-restraints excluded: chain R residue  309 VAL
Chi-restraints excluded: chain R residue  359 ILE
Chi-restraints excluded: chain R residue  367 VAL
Chi-restraints excluded: chain G residue  505 LEU
Chi-restraints excluded: chain G residue  511 LEU
Chi-restraints excluded: chain G residue  537 GLU
Chi-restraints excluded: chain G residue  636 SER
Chi-restraints excluded: chain G residue  651 TYR
Chi-restraints excluded: chain Q residue   56 ILE
Chi-restraints excluded: chain Q residue  176 GLN
Chi-restraints excluded: chain Q residue  178 ASP
Chi-restraints excluded: chain Q residue  190 ILE
Chi-restraints excluded: chain Q residue  203 MET
Chi-restraints excluded: chain Q residue  270 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 118 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 116 optimal weight:    1.9990
   chunk 123 optimal weight:    7.9990
   chunk 103 optimal weight:    8.9990
   chunk 96 optimal weight:    0.7980
   chunk 16 optimal weight:   40.0000
   chunk 27 optimal weight:    6.9990
   chunk 122 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
Q  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.168786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.120588 restraints weight = 14272.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.71
r_work: 0.3237 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.3199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.105   9806  Z= 0.187
  Angle     :  1.062  59.086  13365  Z= 0.538
  Chirality :  0.043   0.347   1541
  Planarity :  0.004   0.056   1697
  Dihedral  :  9.825 148.172   1421
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 20.00 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.24), residues: 1266
  helix:  1.76 (0.20), residues: 709
  sheet:  0.42 (0.48), residues: 109
  loop : -0.43 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG Q  92 
 TYR   0.021   0.001   TYR Q 159 
 PHE   0.049   0.001   PHE R 188 
 TRP   0.046   0.002   TRP G 576 
 HIS   0.005   0.001   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 9804)
  covalent geometry    : angle       1.06223 (13363)
  SS BOND              : bond        0.00086 (    1)
  SS BOND              : angle       0.45606 (    2)
  hydrogen bonds       : bond        0.03550 (  576)
  hydrogen bonds       : angle       4.46684 ( 1674)
  Misc. bond           : bond        0.00041 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4054.32 seconds
wall clock time: 69 minutes 39.36 seconds (4179.36 seconds total)