Starting phenix.real_space_refine
on Wed Sep 17 14:24:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zdt_14669/09_2025/7zdt_14669_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zdt_14669/09_2025/7zdt_14669.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zdt_14669/09_2025/7zdt_14669_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zdt_14669/09_2025/7zdt_14669_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zdt_14669/09_2025/7zdt_14669.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zdt_14669/09_2025/7zdt_14669.map"
  }
  resolution = 2.71
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      30      5.16       5
     C    5761      2.51       5
     N    1584      2.21       5
     O    1624      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9003
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 4425
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4425
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 18, 'TRANS': 553}
    Chain: "D"
      Number of atoms: 4546
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 583, 4546
          Classifications: {'peptide': 583}
          Link IDs: {'PTRANS': 27, 'TRANS': 555}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.82, per 1000 atoms: 0.20
  Number of scatterers: 9003
  At special positions: 0
  Unit cell: (137.268, 77.841, 100.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      30     16.00
     P       3     15.00
     Mg      1     11.99
     O    1624      8.00
     N    1584      7.00
     C    5761      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 343.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2136

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 5 sheets defined
      69.3% alpha, 9.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'C' and resid 1 through 3
      No H-bonds generated for 'chain 'C' and resid 1 through 3'
    Processing helix  chain 'C' and resid 4 through 9
    Processing helix  chain 'C' and resid 10 through 12
      No H-bonds generated for 'chain 'C' and resid 10 through 12'
    Processing helix  chain 'C' and resid 14 through 50
      removed outlier: 3.654A  pdb=" N   LEU C  36 " --> pdb=" O   SER C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 101
      removed outlier: 3.585A  pdb=" N   ILE C  71 " --> pdb=" O   ARG C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 107
      Proline residue:  C 105  - end of helix
      No H-bonds generated for 'chain 'C' and resid 102 through 107'
    Processing helix  chain 'C' and resid 110 through 114
    Processing helix  chain 'C' and resid 115 through 130
      removed outlier: 4.687A  pdb=" N   VAL C 127 " --> pdb=" O   VAL C 123 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ASP C 128 " --> pdb=" O   VAL C 124 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LEU C 130 " --> pdb=" O   ASP C 126 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 130 through 136
      removed outlier: 3.721A  pdb=" N   TYR C 134 " --> pdb=" O   LEU C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 159
      removed outlier: 3.768A  pdb=" N   PHE C 157 " --> pdb=" O   ILE C 153 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   LEU C 158 " --> pdb=" O   GLY C 154 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 209
      Proline residue:  C 178  - end of helix
      removed outlier: 4.649A  pdb=" N   SER C 187 " --> pdb=" O   ARG C 183 " (cutoff:3.500A)
      removed outlier: 5.206A  pdb=" N   THR C 188 " --> pdb=" O   ALA C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 216
      removed outlier: 3.782A  pdb=" N   ILE C 215 " --> pdb=" O   ALA C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 218 through 269
      removed outlier: 3.596A  pdb=" N   SER C 267 " --> pdb=" O   LEU C 263 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   GLY C 268 " --> pdb=" O   TRP C 264 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   GLY C 269 " --> pdb=" O   MET C 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 277 through 291
      removed outlier: 4.450A  pdb=" N   ALA C 281 " --> pdb=" O   GLY C 277 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   PHE C 291 " --> pdb=" O   ALA C 287 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 294 through 303
      removed outlier: 4.094A  pdb=" N   THR C 298 " --> pdb=" O   LEU C 294 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   GLY C 299 " --> pdb=" O   ALA C 295 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   PHE C 301 " --> pdb=" O   VAL C 297 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   HIS C 303 " --> pdb=" O   GLY C 299 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 303 through 319
    Processing helix  chain 'C' and resid 378 through 386
    Processing helix  chain 'C' and resid 405 through 407
      No H-bonds generated for 'chain 'C' and resid 405 through 407'
    Processing helix  chain 'C' and resid 408 through 414
    Processing helix  chain 'C' and resid 429 through 435
    Processing helix  chain 'C' and resid 442 through 454
    Processing helix  chain 'C' and resid 455 through 460
      removed outlier: 3.547A  pdb=" N   GLU C 460 " --> pdb=" O   LYS C 457 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 462 through 466
    Processing helix  chain 'C' and resid 476 through 492
      removed outlier: 3.519A  pdb=" N   ASP C 492 " --> pdb=" O   ALA C 488 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 506 through 521
    Processing helix  chain 'C' and resid 555 through 563
    Processing helix  chain 'C' and resid 564 through 571
      removed outlier: 3.585A  pdb=" N   GLN C 568 " --> pdb=" O   GLY C 564 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 16
    Processing helix  chain 'D' and resid 17 through 19
      No H-bonds generated for 'chain 'D' and resid 17 through 19'
    Processing helix  chain 'D' and resid 20 through 55
    Processing helix  chain 'D' and resid 63 through 115
      removed outlier: 3.702A  pdb=" N   GLY D 110 " --> pdb=" O   LEU D 106 " (cutoff:3.500A)
      Proline residue:  D 111  - end of helix
    Processing helix  chain 'D' and resid 118 through 127
    Processing helix  chain 'D' and resid 127 through 132
    Processing helix  chain 'D' and resid 133 through 139
    Processing helix  chain 'D' and resid 139 through 157
      removed outlier: 4.767A  pdb=" N   ALA D 145 " --> pdb=" O   LEU D 141 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LEU D 146 " --> pdb=" O   PRO D 142 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL D 148 " --> pdb=" O   MET D 144 " (cutoff:3.500A)
      Proline residue:  D 151  - end of helix
    Processing helix  chain 'D' and resid 162 through 173
      removed outlier: 3.534A  pdb=" N   ALA D 166 " --> pdb=" O   ASN D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 174 through 184
      removed outlier: 4.305A  pdb=" N   LEU D 178 " --> pdb=" O   PRO D 174 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 186 through 211
    Processing helix  chain 'D' and resid 211 through 219
    Processing helix  chain 'D' and resid 220 through 274
      removed outlier: 3.652A  pdb=" N   LEU D 245 " --> pdb=" O   GLU D 241 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 328
      removed outlier: 3.522A  pdb=" N   GLY D 290 " --> pdb=" O   THR D 286 " (cutoff:3.500A)
      Proline residue:  D 298  - end of helix
      removed outlier: 3.625A  pdb=" N   PHE D 301 " --> pdb=" O   ALA D 297 " (cutoff:3.500A)
      Proline residue:  D 303  - end of helix
      removed outlier: 3.703A  pdb=" N   HIS D 312 " --> pdb=" O   GLY D 308 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ALA D 313 " --> pdb=" O   THR D 309 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   SER D 323 " --> pdb=" O   GLY D 319 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   LEU D 324 " --> pdb=" O   ALA D 320 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 388 through 397
      removed outlier: 3.570A  pdb=" N   LEU D 392 " --> pdb=" O   GLY D 388 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU D 393 " --> pdb=" O   LYS D 389 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 416
      No H-bonds generated for 'chain 'D' and resid 414 through 416'
    Processing helix  chain 'D' and resid 417 through 423
      removed outlier: 3.625A  pdb=" N   LYS D 423 " --> pdb=" O   GLU D 419 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 438 through 444
    Processing helix  chain 'D' and resid 451 through 462
    Processing helix  chain 'D' and resid 473 through 477
    Processing helix  chain 'D' and resid 487 through 500
    Processing helix  chain 'D' and resid 517 through 533
      removed outlier: 3.546A  pdb=" N   GLN D 522 " --> pdb=" O   ALA D 518 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 566 through 573
      removed outlier: 3.997A  pdb=" N   VAL D 572 " --> pdb=" O   ALA D 568 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 574 through 583
      removed outlier: 3.885A  pdb=" N   HIS D 583 " --> pdb=" O   THR D 579 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 363
      removed outlier: 5.662A  pdb=" N   LYS C 357 " --> pdb=" O   PHE C 346 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   PHE C 346 " --> pdb=" O   LYS C 357 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   LEU C 361 " --> pdb=" O   ARG C 342 " (cutoff:3.500A)
      removed outlier: 5.581A  pdb=" N   ARG C 342 " --> pdb=" O   LEU C 361 " (cutoff:3.500A)
      removed outlier: 7.347A  pdb=" N   VAL C 363 " --> pdb=" O   THR C 340 " (cutoff:3.500A)
      removed outlier: 5.422A  pdb=" N   THR C 340 " --> pdb=" O   VAL C 363 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLU C 396 " --> pdb=" O   ARG C 342 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 416 through 419
      removed outlier: 6.261A  pdb=" N   SER C 417 " --> pdb=" O   LEU C 497 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   ASP C 499 " --> pdb=" O   SER C 417 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   VAL C 419 " --> pdb=" O   ASP C 499 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   VAL C 496 " --> pdb=" O   LEU C 527 " (cutoff:3.500A)
      removed outlier: 7.522A  pdb=" N   VAL C 529 " --> pdb=" O   VAL C 496 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LEU C 498 " --> pdb=" O   VAL C 529 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   ILE C 369 " --> pdb=" O   MET C 528 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLN C 541 " --> pdb=" O   HIS C 368 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLU C 552 " --> pdb=" O   VAL C 544 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 364 through 373
      removed outlier: 6.630A  pdb=" N   ILE D 357 " --> pdb=" O   LEU D 365 " (cutoff:3.500A)
      removed outlier: 5.108A  pdb=" N   GLY D 367 " --> pdb=" O   LEU D 355 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   LEU D 355 " --> pdb=" O   GLY D 367 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   LEU D 369 " --> pdb=" O   GLU D 353 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   GLU D 353 " --> pdb=" O   LEU D 369 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   PHE D 371 " --> pdb=" O   GLU D 351 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   GLU D 351 " --> pdb=" O   PHE D 371 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   SER D 401 " --> pdb=" O   THR D 358 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 364 through 373
      removed outlier: 6.630A  pdb=" N   ILE D 357 " --> pdb=" O   LEU D 365 " (cutoff:3.500A)
      removed outlier: 5.108A  pdb=" N   GLY D 367 " --> pdb=" O   LEU D 355 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   LEU D 355 " --> pdb=" O   GLY D 367 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   LEU D 369 " --> pdb=" O   GLU D 353 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   GLU D 353 " --> pdb=" O   LEU D 369 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   PHE D 371 " --> pdb=" O   GLU D 351 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   GLU D 351 " --> pdb=" O   PHE D 371 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 425 through 428
      removed outlier: 6.429A  pdb=" N   SER D 426 " --> pdb=" O   LEU D 508 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LEU D 507 " --> pdb=" O   LEU D 538 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   VAL D 540 " --> pdb=" O   LEU D 507 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   LEU D 509 " --> pdb=" O   VAL D 540 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   ARG D 378 " --> pdb=" O   VAL D 552 " (cutoff:3.500A)
      removed outlier: 8.023A  pdb=" N   TRP D 554 " --> pdb=" O   ARG D 378 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   VAL D 380 " --> pdb=" O   TRP D 554 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   MET D 556 " --> pdb=" O   VAL D 380 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   VAL D 382 " --> pdb=" O   MET D 556 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   VAL D 555 " --> pdb=" O   ILE D 562 " (cutoff:3.500A)

    575 hydrogen bonds defined for protein.
    1689 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: 1.70

  Time building geometry restraints manager: 1.06 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1923
        1.33 -     1.45: 1980
        1.45 -     1.57: 5217
        1.57 -     1.69: 5
        1.69 -     1.81: 57
  Bond restraints: 9182
  Sorted by residual:
  bond pdb=" N   GLN C 500 "
       pdb=" CA  GLN C 500 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 9.10e-03 1.21e+04 1.17e+01
  bond pdb=" N   GLN D 302 "
       pdb=" CA  GLN D 302 "
    ideal  model  delta    sigma   weight residual
    1.462  1.486 -0.024 7.70e-03 1.69e+04 9.48e+00
  bond pdb=" N   PHE D 159 "
       pdb=" CA  PHE D 159 "
    ideal  model  delta    sigma   weight residual
    1.461  1.488 -0.026 9.20e-03 1.18e+04 8.26e+00
  bond pdb=" N   GLU C 460 "
       pdb=" CA  GLU C 460 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.037 1.34e-02 5.57e+03 7.62e+00
  bond pdb=" N   GLN C 351 "
       pdb=" CA  GLN C 351 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.29e-02 6.01e+03 6.96e+00
  ... (remaining 9177 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 11956
        1.51 -     3.02: 437
        3.02 -     4.54: 69
        4.54 -     6.05: 14
        6.05 -     7.56: 4
  Bond angle restraints: 12480
  Sorted by residual:
  angle pdb=" PB  ATP C 602 "
        pdb=" O3B ATP C 602 "
        pdb=" PG  ATP C 602 "
      ideal   model   delta    sigma   weight residual
     139.87  133.93    5.94 1.00e+00 1.00e+00 3.53e+01
  angle pdb=" PA  ATP C 602 "
        pdb=" O3A ATP C 602 "
        pdb=" PB  ATP C 602 "
      ideal   model   delta    sigma   weight residual
     136.83  132.97    3.86 1.00e+00 1.00e+00 1.49e+01
  angle pdb=" CA  GLN C 500 "
        pdb=" C   GLN C 500 "
        pdb=" O   GLN C 500 "
      ideal   model   delta    sigma   weight residual
     120.47  117.97    2.50 6.90e-01 2.10e+00 1.31e+01
  angle pdb=" CA  THR C 502 "
        pdb=" C   THR C 502 "
        pdb=" O   THR C 502 "
      ideal   model   delta    sigma   weight residual
     122.63  117.97    4.66 1.29e+00 6.01e-01 1.31e+01
  angle pdb=" CA  ASP C 461 "
        pdb=" C   ASP C 461 "
        pdb=" N   ALA C 462 "
      ideal   model   delta    sigma   weight residual
     119.98  117.02    2.96 8.50e-01 1.38e+00 1.21e+01
  ... (remaining 12475 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.15: 4892
       16.15 -    32.29: 461
       32.29 -    48.43: 114
       48.43 -    64.58: 22
       64.58 -    80.72: 9
  Dihedral angle restraints: 5498
    sinusoidal: 2185
      harmonic: 3313
  Sorted by residual:
  dihedral pdb=" CA  ARG C 473 "
           pdb=" C   ARG C 473 "
           pdb=" N   GLN C 474 "
           pdb=" CA  GLN C 474 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.60   20.40     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" CA  LEU C 106 "
           pdb=" C   LEU C 106 "
           pdb=" N   SER C 107 "
           pdb=" CA  SER C 107 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.23  -18.77     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  ARG C 136 "
           pdb=" C   ARG C 136 "
           pdb=" N   VAL C 137 "
           pdb=" CA  VAL C 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.40   17.60     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 5495 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1098
       0.044 -    0.087: 255
       0.087 -    0.131: 76
       0.131 -    0.175: 17
       0.175 -    0.218: 3
  Chirality restraints: 1449
  Sorted by residual:
  chirality pdb=" CA  PHE C 181 "
            pdb=" N   PHE C 181 "
            pdb=" C   PHE C 181 "
            pdb=" CB  PHE C 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  ARG C 534 "
            pdb=" N   ARG C 534 "
            pdb=" C   ARG C 534 "
            pdb=" CB  ARG C 534 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CA  ARG C 538 "
            pdb=" N   ARG C 538 "
            pdb=" C   ARG C 538 "
            pdb=" CB  ARG C 538 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.19 2.00e-01 2.50e+01 9.48e-01
  ... (remaining 1446 not shown)

  Planarity restraints: 1593
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C  61 "    0.034 5.00e-02 4.00e+02   5.18e-02 4.30e+00
        pdb=" N   PRO C  62 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO C  62 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO C  62 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D 158 "   -0.009 2.00e-02 2.50e+03   1.85e-02 3.44e+00
        pdb=" C   ILE D 158 "    0.032 2.00e-02 2.50e+03
        pdb=" O   ILE D 158 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   PHE D 159 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE D 159 "    0.009 2.00e-02 2.50e+03   1.81e-02 3.28e+00
        pdb=" C   PHE D 159 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   PHE D 159 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PRO D 160 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1590 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 48
        2.54 -     3.13: 6728
        3.13 -     3.72: 14401
        3.72 -     4.31: 20830
        4.31 -     4.90: 34918
  Nonbonded interactions: 76925
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN C 421 "
            pdb="MG    MG C 601 "
     model   vdw
     1.945 2.170
  nonbonded pdb=" N   GLU D 545 "
            pdb=" OE1 GLU D 545 "
     model   vdw
     2.204 3.120
  nonbonded pdb="MG    MG C 601 "
            pdb=" O1B ATP C 602 "
     model   vdw
     2.215 2.170
  nonbonded pdb=" OG  SER C 380 "
            pdb="MG    MG C 601 "
     model   vdw
     2.228 2.170
  nonbonded pdb=" NH2 ARG D 337 "
            pdb=" OE1 GLU D 419 "
     model   vdw
     2.257 3.120
  ... (remaining 76920 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:             1.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.240
  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:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
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      :  0.005   0.047   9182  Z= 0.265
  Angle     :  0.662   7.561  12480  Z= 0.416
  Chirality :  0.044   0.218   1449
  Planarity :  0.004   0.052   1593
  Dihedral  : 13.922  80.724   3362
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.81 (0.23), residues: 1151
  helix: -0.62 (0.18), residues: 712
  sheet:  0.22 (0.67), residues: 63
  loop : -0.10 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 337 
 TYR   0.015   0.002   TYR D  88 
 PHE   0.015   0.001   PHE D 467 
 TRP   0.009   0.001   TRP C 390 
 HIS   0.005   0.001   HIS C 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 ( 9182)
  covalent geometry    : angle       0.66212 (12480)
  hydrogen bonds       : bond        0.24294 (  574)
  hydrogen bonds       : angle       7.87077 ( 1689)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.374 
Fit side-chains
REVERT: D   11 ARG cc_start: 0.7955 (ttm110) cc_final: 0.7743 (ttp-170)
REVERT: D  523 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7601 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.7955
  time to fit residues: 105.4981
Evaluate side-chains
  97 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
C 210 GLN
C 474 GLN
D 115 GLN
D 557 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.122252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.095721 restraints weight = 11108.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 1.70
r_work: 0.2925 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2804 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8790
moved from start:          0.1367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9182  Z= 0.160
  Angle     :  0.554   6.130  12480  Z= 0.292
  Chirality :  0.040   0.175   1449
  Planarity :  0.005   0.050   1593
  Dihedral  :  7.139  84.752   1292
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  7.47 %
    Favored  : 91.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.24), residues: 1151
  helix:  1.34 (0.19), residues: 715
  sheet:  0.14 (0.65), residues: 63
  loop :  0.18 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 337 
 TYR   0.016   0.002   TYR D  88 
 PHE   0.017   0.002   PHE C  89 
 TRP   0.020   0.002   TRP D 427 
 HIS   0.006   0.001   HIS D 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 9182)
  covalent geometry    : angle       0.55369 (12480)
  hydrogen bonds       : bond        0.06086 (  574)
  hydrogen bonds       : angle       4.38518 ( 1689)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: C  275 GLN cc_start: 0.8333 (mt0) cc_final: 0.8102 (mm-40)
REVERT: D   11 ARG cc_start: 0.8590 (ttm110) cc_final: 0.8337 (ttp-110)
REVERT: D  384 ARG cc_start: 0.8200 (mmm-85) cc_final: 0.7976 (mmt90)
  outliers start: 13
  outliers final: 1
  residues processed: 112
  average time/residue: 0.8355
  time to fit residues: 98.4666
Evaluate side-chains
  96 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  172 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9990
   chunk 91 optimal weight:    8.9990
   chunk 55 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   chunk 75 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
D 115 GLN
D 557 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.123651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.098547 restraints weight = 11075.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 1.48
r_work: 0.2935 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8803
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9182  Z= 0.144
  Angle     :  0.515   7.767  12480  Z= 0.268
  Chirality :  0.039   0.169   1449
  Planarity :  0.004   0.048   1593
  Dihedral  :  7.013  80.708   1292
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  :  9.50 %
    Favored  : 88.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.25), residues: 1151
  helix:  2.04 (0.19), residues: 714
  sheet:  0.10 (0.67), residues: 62
  loop :  0.28 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 337 
 TYR   0.016   0.001   TYR D  88 
 PHE   0.017   0.001   PHE C  89 
 TRP   0.017   0.001   TRP D  81 
 HIS   0.006   0.001   HIS D 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 9182)
  covalent geometry    : angle       0.51529 (12480)
  hydrogen bonds       : bond        0.05313 (  574)
  hydrogen bonds       : angle       4.06624 ( 1689)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.371 
Fit side-chains
REVERT: C   60 MET cc_start: 0.7616 (mmm) cc_final: 0.7373 (mmm)
REVERT: C  267 SER cc_start: 0.9040 (OUTLIER) cc_final: 0.8699 (m)
REVERT: C  474 GLN cc_start: 0.8206 (tp40) cc_final: 0.7910 (mp10)
REVERT: D   11 ARG cc_start: 0.8592 (ttm110) cc_final: 0.8331 (ttp-110)
  outliers start: 18
  outliers final: 8
  residues processed: 106
  average time/residue: 0.7903
  time to fit residues: 88.3658
Evaluate side-chains
  104 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  139 SER
Chi-restraints excluded: chain C residue  267 SER
Chi-restraints excluded: chain C residue  297 VAL
Chi-restraints excluded: chain C residue  456 GLU
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue    4 SER
Chi-restraints excluded: chain D residue  152 LEU
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  342 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 40 optimal weight:    0.0770
   chunk 60 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0020
   chunk 97 optimal weight:    0.7980
   chunk 114 optimal weight:    6.9990
   chunk 104 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 102 optimal weight:    4.9990
   chunk 95 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    0.9750

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

Flipped N/Q/H residues before XYZ refinement:
D 557 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.122727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.097163 restraints weight = 11198.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 1.52
r_work: 0.2966 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8809
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   9182  Z= 0.147
  Angle     :  0.507   6.139  12480  Z= 0.266
  Chirality :  0.039   0.166   1449
  Planarity :  0.004   0.045   1593
  Dihedral  :  6.926  79.127   1292
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  :  9.93 %
    Favored  : 87.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.28 (0.25), residues: 1151
  helix:  2.30 (0.19), residues: 714
  sheet:  0.13 (0.68), residues: 62
  loop :  0.29 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 374 
 TYR   0.016   0.001   TYR D  88 
 PHE   0.014   0.001   PHE D 467 
 TRP   0.016   0.001   TRP D 427 
 HIS   0.006   0.001   HIS D 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 9182)
  covalent geometry    : angle       0.50720 (12480)
  hydrogen bonds       : bond        0.05054 (  574)
  hydrogen bonds       : angle       3.96139 ( 1689)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
REVERT: C  267 SER cc_start: 0.9063 (OUTLIER) cc_final: 0.8710 (m)
REVERT: C  297 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8803 (m)
REVERT: C  453 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8410 (m)
REVERT: D   11 ARG cc_start: 0.8566 (ttm110) cc_final: 0.8308 (ttp-110)
REVERT: D   92 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8993 (tt0)
  outliers start: 21
  outliers final: 11
  residues processed: 107
  average time/residue: 0.8004
  time to fit residues: 90.3295
Evaluate side-chains
  110 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  139 SER
Chi-restraints excluded: chain C residue  220 ASP
Chi-restraints excluded: chain C residue  267 SER
Chi-restraints excluded: chain C residue  297 VAL
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  456 GLU
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue    4 SER
Chi-restraints excluded: chain D residue   92 GLN
Chi-restraints excluded: chain D residue  152 LEU
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  342 LEU
Chi-restraints excluded: chain D residue  427 TRP
Chi-restraints excluded: chain D residue  544 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 90 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 83 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
D 543 GLN
D 557 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.122988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.096502 restraints weight = 11125.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 1.70
r_work: 0.2924 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2803 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8753
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   9182  Z= 0.143
  Angle     :  0.500   6.182  12480  Z= 0.261
  Chirality :  0.039   0.161   1449
  Planarity :  0.004   0.043   1593
  Dihedral  :  6.886  79.718   1292
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 10.89 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.40 (0.25), residues: 1151
  helix:  2.43 (0.19), residues: 713
  sheet:  0.07 (0.68), residues: 62
  loop :  0.26 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 337 
 TYR   0.016   0.001   TYR D  88 
 PHE   0.016   0.001   PHE C  89 
 TRP   0.016   0.001   TRP D  81 
 HIS   0.006   0.001   HIS D 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 9182)
  covalent geometry    : angle       0.49972 (12480)
  hydrogen bonds       : bond        0.04914 (  574)
  hydrogen bonds       : angle       3.89627 ( 1689)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.344 
Fit side-chains
REVERT: C  267 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8625 (m)
REVERT: C  297 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8765 (m)
REVERT: C  453 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8276 (m)
REVERT: D  419 GLU cc_start: 0.8091 (mp0) cc_final: 0.7583 (mp0)
  outliers start: 24
  outliers final: 12
  residues processed: 105
  average time/residue: 0.7637
  time to fit residues: 84.6194
Evaluate side-chains
  106 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  139 SER
Chi-restraints excluded: chain C residue  149 MET
Chi-restraints excluded: chain C residue  220 ASP
Chi-restraints excluded: chain C residue  267 SER
Chi-restraints excluded: chain C residue  297 VAL
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  456 GLU
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue    4 SER
Chi-restraints excluded: chain D residue  152 LEU
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  227 SER
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  342 LEU
Chi-restraints excluded: chain D residue  427 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 109 optimal weight:    4.9990
   chunk 59 optimal weight:    0.6980
   chunk 113 optimal weight:    5.9990
   chunk 90 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 77 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 110 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
C 408 ASN
C 541 GLN
D 557 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.120953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.095134 restraints weight = 11203.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 1.55
r_work: 0.2899 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2781 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8834
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   9182  Z= 0.204
  Angle     :  0.551   6.842  12480  Z= 0.285
  Chirality :  0.042   0.160   1449
  Planarity :  0.004   0.042   1593
  Dihedral  :  7.052  79.447   1292
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 11.63 %
    Favored  : 85.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.19 (0.25), residues: 1151
  helix:  2.23 (0.19), residues: 720
  sheet: -0.02 (0.68), residues: 63
  loop :  0.22 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 337 
 TYR   0.018   0.002   TYR D  88 
 PHE   0.020   0.002   PHE D 467 
 TRP   0.015   0.002   TRP D 427 
 HIS   0.007   0.001   HIS D 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 9182)
  covalent geometry    : angle       0.55106 (12480)
  hydrogen bonds       : bond        0.05411 (  574)
  hydrogen bonds       : angle       4.00238 ( 1689)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.354 
Fit side-chains
REVERT: C  267 SER cc_start: 0.9075 (OUTLIER) cc_final: 0.8668 (m)
REVERT: C  275 GLN cc_start: 0.8415 (mt0) cc_final: 0.8186 (mm-40)
REVERT: C  297 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8853 (m)
REVERT: C  453 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8445 (m)
REVERT: C  521 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8173 (mtt)
REVERT: D  407 ARG cc_start: 0.8497 (mtm110) cc_final: 0.8260 (mtm180)
REVERT: D  419 GLU cc_start: 0.8043 (mp0) cc_final: 0.7744 (mp0)
  outliers start: 24
  outliers final: 12
  residues processed: 103
  average time/residue: 0.7550
  time to fit residues: 82.0252
Evaluate side-chains
  109 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  139 SER
Chi-restraints excluded: chain C residue  149 MET
Chi-restraints excluded: chain C residue  220 ASP
Chi-restraints excluded: chain C residue  267 SER
Chi-restraints excluded: chain C residue  297 VAL
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  456 GLU
Chi-restraints excluded: chain C residue  521 MET
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue    4 SER
Chi-restraints excluded: chain D residue  152 LEU
Chi-restraints excluded: chain D residue  227 SER
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  342 LEU
Chi-restraints excluded: chain D residue  427 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 91 optimal weight:   10.0000
   chunk 86 optimal weight:    1.9990
   chunk 101 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
D 557 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.122467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.095920 restraints weight = 11209.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 1.70
r_work: 0.2933 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2813 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8785
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9182  Z= 0.146
  Angle     :  0.499   6.203  12480  Z= 0.261
  Chirality :  0.039   0.153   1449
  Planarity :  0.004   0.040   1593
  Dihedral  :  6.925  80.331   1292
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.38 %
    Favored  : 85.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.38 (0.25), residues: 1151
  helix:  2.41 (0.19), residues: 714
  sheet:  0.05 (0.69), residues: 62
  loop :  0.26 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 337 
 TYR   0.015   0.001   TYR D  88 
 PHE   0.016   0.001   PHE C  89 
 TRP   0.016   0.002   TRP D  81 
 HIS   0.005   0.001   HIS D 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 9182)
  covalent geometry    : angle       0.49874 (12480)
  hydrogen bonds       : bond        0.04939 (  574)
  hydrogen bonds       : angle       3.89345 ( 1689)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.318 
Fit side-chains
REVERT: C  267 SER cc_start: 0.9046 (OUTLIER) cc_final: 0.8640 (m)
REVERT: C  275 GLN cc_start: 0.8448 (mt0) cc_final: 0.8143 (mm-40)
REVERT: C  297 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8786 (m)
REVERT: C  453 VAL cc_start: 0.8639 (OUTLIER) cc_final: 0.8347 (m)
REVERT: D  407 ARG cc_start: 0.8478 (mtm110) cc_final: 0.8217 (mtm180)
  outliers start: 19
  outliers final: 11
  residues processed: 102
  average time/residue: 0.8001
  time to fit residues: 85.9294
Evaluate side-chains
  104 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  139 SER
Chi-restraints excluded: chain C residue  149 MET
Chi-restraints excluded: chain C residue  220 ASP
Chi-restraints excluded: chain C residue  267 SER
Chi-restraints excluded: chain C residue  297 VAL
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue    4 SER
Chi-restraints excluded: chain D residue  152 LEU
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  227 SER
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  342 LEU
Chi-restraints excluded: chain D residue  427 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 102 optimal weight:    0.0870
   chunk 17 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 7 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 61 optimal weight:    0.4980
   chunk 93 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 52 optimal weight:    0.7980
   chunk 1 optimal weight:    5.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
D 115 GLN
D 482 GLN
D 557 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.124285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.098882 restraints weight = 11107.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 1.52
r_work: 0.2991 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8784
moved from start:          0.2126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9182  Z= 0.118
  Angle     :  0.476   6.739  12480  Z= 0.248
  Chirality :  0.038   0.151   1449
  Planarity :  0.004   0.040   1593
  Dihedral  :  6.768  82.414   1292
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 12.91 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.58 (0.25), residues: 1151
  helix:  2.60 (0.19), residues: 713
  sheet:  0.09 (0.69), residues: 62
  loop :  0.30 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 560 
 TYR   0.013   0.001   TYR D  88 
 PHE   0.016   0.001   PHE C  89 
 TRP   0.018   0.001   TRP D  81 
 HIS   0.004   0.001   HIS D 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 9182)
  covalent geometry    : angle       0.47628 (12480)
  hydrogen bonds       : bond        0.04528 (  574)
  hydrogen bonds       : angle       3.79246 ( 1689)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.367 
Fit side-chains
REVERT: C  267 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8695 (m)
REVERT: C  297 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8805 (m)
REVERT: D  407 ARG cc_start: 0.8489 (mtm110) cc_final: 0.8261 (mtm180)
  outliers start: 20
  outliers final: 13
  residues processed: 106
  average time/residue: 0.8111
  time to fit residues: 90.5362
Evaluate side-chains
  108 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  139 SER
Chi-restraints excluded: chain C residue  149 MET
Chi-restraints excluded: chain C residue  220 ASP
Chi-restraints excluded: chain C residue  267 SER
Chi-restraints excluded: chain C residue  297 VAL
Chi-restraints excluded: chain C residue  456 GLU
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue    4 SER
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  227 SER
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  342 LEU
Chi-restraints excluded: chain D residue  427 TRP
Chi-restraints excluded: chain D residue  544 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 110 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 57 optimal weight:    0.5980
   chunk 15 optimal weight:    0.4980
   chunk 100 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C 408 ASN
D 482 GLN
D 557 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.124058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.098572 restraints weight = 11171.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 1.53
r_work: 0.2981 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2865 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8787
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9182  Z= 0.126
  Angle     :  0.487   6.271  12480  Z= 0.254
  Chirality :  0.038   0.152   1449
  Planarity :  0.004   0.039   1593
  Dihedral  :  6.752  84.782   1292
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 13.23 %
    Favored  : 84.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.61 (0.25), residues: 1151
  helix:  2.64 (0.19), residues: 713
  sheet:  0.17 (0.69), residues: 62
  loop :  0.27 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D 337 
 TYR   0.014   0.001   TYR D  88 
 PHE   0.016   0.001   PHE C  89 
 TRP   0.017   0.001   TRP D  81 
 HIS   0.005   0.001   HIS D 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 9182)
  covalent geometry    : angle       0.48705 (12480)
  hydrogen bonds       : bond        0.04587 (  574)
  hydrogen bonds       : angle       3.78528 ( 1689)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.361 
Fit side-chains
REVERT: C  267 SER cc_start: 0.9028 (OUTLIER) cc_final: 0.8692 (m)
REVERT: C  297 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8807 (m)
REVERT: D  407 ARG cc_start: 0.8508 (mtm110) cc_final: 0.8277 (mtm180)
  outliers start: 19
  outliers final: 13
  residues processed: 102
  average time/residue: 0.8330
  time to fit residues: 89.3357
Evaluate side-chains
  105 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  139 SER
Chi-restraints excluded: chain C residue  149 MET
Chi-restraints excluded: chain C residue  220 ASP
Chi-restraints excluded: chain C residue  267 SER
Chi-restraints excluded: chain C residue  297 VAL
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue    4 SER
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  227 SER
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  342 LEU
Chi-restraints excluded: chain D residue  427 TRP
Chi-restraints excluded: chain D residue  544 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 113 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0980
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
D 482 GLN
D 557 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.124685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.099247 restraints weight = 11022.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 1.51
r_work: 0.2995 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8777
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9182  Z= 0.121
  Angle     :  0.487   7.747  12480  Z= 0.252
  Chirality :  0.038   0.151   1449
  Planarity :  0.004   0.039   1593
  Dihedral  :  6.657  87.388   1292
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 13.87 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.68 (0.25), residues: 1151
  helix:  2.69 (0.19), residues: 713
  sheet:  0.21 (0.70), residues: 62
  loop :  0.29 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 337 
 TYR   0.014   0.001   TYR D  88 
 PHE   0.016   0.001   PHE C  89 
 TRP   0.017   0.001   TRP D  81 
 HIS   0.005   0.001   HIS D 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9182)
  covalent geometry    : angle       0.48675 (12480)
  hydrogen bonds       : bond        0.04492 (  574)
  hydrogen bonds       : angle       3.75510 ( 1689)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.384 
Fit side-chains
REVERT: C  177 MET cc_start: 0.8882 (mtp) cc_final: 0.8659 (ttt)
REVERT: C  297 VAL cc_start: 0.9013 (OUTLIER) cc_final: 0.8784 (m)
REVERT: D  407 ARG cc_start: 0.8493 (mtm110) cc_final: 0.8265 (mtm180)
  outliers start: 18
  outliers final: 14
  residues processed: 98
  average time/residue: 0.7913
  time to fit residues: 81.5696
Evaluate side-chains
  105 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  139 SER
Chi-restraints excluded: chain C residue  149 MET
Chi-restraints excluded: chain C residue  220 ASP
Chi-restraints excluded: chain C residue  297 VAL
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue    4 SER
Chi-restraints excluded: chain D residue  152 LEU
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  227 SER
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  342 LEU
Chi-restraints excluded: chain D residue  427 TRP
Chi-restraints excluded: chain D residue  544 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 99 optimal weight:    4.9990
   chunk 90 optimal weight:    5.9990
   chunk 95 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9990
   chunk 106 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
D 115 GLN
D 482 GLN
D 557 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.123268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.096378 restraints weight = 10984.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 1.69
r_work: 0.2906 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2785 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8741
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9182  Z= 0.133
  Angle     :  0.496   8.349  12480  Z= 0.258
  Chirality :  0.039   0.151   1449
  Planarity :  0.004   0.041   1593
  Dihedral  :  6.669  89.513   1292
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 13.77 %
    Favored  : 84.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.63 (0.25), residues: 1151
  helix:  2.65 (0.19), residues: 713
  sheet:  0.25 (0.70), residues: 62
  loop :  0.26 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 374 
 TYR   0.015   0.001   TYR D  88 
 PHE   0.016   0.001   PHE C  89 
 TRP   0.016   0.001   TRP D  81 
 HIS   0.005   0.001   HIS D 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9182)
  covalent geometry    : angle       0.49555 (12480)
  hydrogen bonds       : bond        0.04627 (  574)
  hydrogen bonds       : angle       3.76873 ( 1689)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3203.95 seconds
wall clock time: 55 minutes 22.60 seconds (3322.60 seconds total)