Starting phenix.real_space_refine
on Tue Mar  3 23:22:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zda_14639/03_2026/7zda_14639_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zda_14639/03_2026/7zda_14639.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zda_14639/03_2026/7zda_14639.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zda_14639/03_2026/7zda_14639.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zda_14639/03_2026/7zda_14639_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zda_14639/03_2026/7zda_14639_neut.cif"
  }
  resolution = 3.17
  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=   0.001 sd=   0.004
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       6      5.49       5
     Mg      2      5.21       5
     S      29      5.16       5
     C    5781      2.51       5
     N    1592      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9052
  Number of models: 1
  Model: ""
    Number of chains: 4
    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: 4563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 587, 4563
          Classifications: {'peptide': 587}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 27, 'TRANS': 559}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 17
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'PO3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      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: 2.27, per 1000 atoms: 0.25
  Number of scatterers: 9052
  At special positions: 0
  Unit cell: (119.691, 80.352, 111.321, 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      29     16.00
     P       6     15.00
     Mg      2     11.99
     O    1642      8.00
     N    1592      7.00
     C    5781      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: 0.62
  Conformation dependent library (CDL) restraints added in 292.4 milliseconds
  

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2144

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 5 sheets defined
      66.9% alpha, 8.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'C' and resid 7 through 13
      removed outlier: 3.782A  pdb=" N   ARG C  13 " --> pdb=" O   ALA C   9 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 14 through 50
      removed outlier: 3.609A  pdb=" N   LEU C  29 " --> pdb=" O   ALA C  25 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU C  36 " --> pdb=" O   SER C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 102
      removed outlier: 3.598A  pdb=" N   ARG C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   HIS C  85 " --> pdb=" O   ARG C  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 107
    Processing helix  chain 'C' and resid 115 through 132
      removed outlier: 3.655A  pdb=" N   LEU C 120 " --> pdb=" O   GLN C 116 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   ASN C 121 " --> pdb=" O   GLY C 117 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   HIS C 132 " --> pdb=" O   ASP C 128 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 137
    Processing helix  chain 'C' and resid 137 through 157
      removed outlier: 3.531A  pdb=" N   VAL C 146 " --> pdb=" O   VAL C 142 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL C 150 " --> pdb=" O   VAL C 146 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   PHE C 157 " --> pdb=" O   ILE C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 185
      Proline residue:  C 178  - end of helix
    Processing helix  chain 'C' and resid 185 through 209
      removed outlier: 3.584A  pdb=" N   GLY C 197 " --> pdb=" O   THR C 193 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 216
      removed outlier: 3.566A  pdb=" N   ILE C 215 " --> pdb=" O   ALA C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 265
      removed outlier: 3.540A  pdb=" N   GLN C 225 " --> pdb=" O   ARG C 221 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LEU C 252 " --> pdb=" O   GLN C 248 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL C 259 " --> pdb=" O   GLY C 255 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   MET C 262 " --> pdb=" O   ALA C 258 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 266 through 268
      No H-bonds generated for 'chain 'C' and resid 266 through 268'
    Processing helix  chain 'C' and resid 277 through 290
      removed outlier: 4.394A  pdb=" N   ALA C 281 " --> pdb=" O   GLY C 277 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 291 through 293
      No H-bonds generated for 'chain 'C' and resid 291 through 293'
    Processing helix  chain 'C' and resid 296 through 298
      No H-bonds generated for 'chain 'C' and resid 296 through 298'
    Processing helix  chain 'C' and resid 299 through 319
      removed outlier: 3.595A  pdb=" N   LEU C 317 " --> pdb=" O   ARG C 313 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 378 through 387
      removed outlier: 3.586A  pdb=" N   GLN C 384 " --> pdb=" O   SER C 380 " (cutoff:3.500A)
    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 415
      removed outlier: 3.883A  pdb=" N   GLN C 414 " --> pdb=" O   ALA C 410 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 429 through 436
      removed outlier: 3.604A  pdb=" N   LEU C 436 " --> pdb=" O   ASP C 432 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 442 through 453
      removed outlier: 3.685A  pdb=" N   ILE C 449 " --> pdb=" O   ALA C 445 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 455 through 459
      removed outlier: 3.562A  pdb=" N   LEU C 458 " --> pdb=" O   LEU C 455 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 462 through 466
    Processing helix  chain 'C' and resid 476 through 491
    Processing helix  chain 'C' and resid 506 through 521
    Processing helix  chain 'C' and resid 555 through 562
    Processing helix  chain 'C' and resid 564 through 571
      removed outlier: 3.647A  pdb=" N   LYS C 570 " --> pdb=" O   TYR C 566 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 17
      removed outlier: 3.536A  pdb=" N   GLU D   8 " --> pdb=" O   SER D   4 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ARG D  11 " --> pdb=" O   LYS D   7 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 22 through 54
      removed outlier: 3.613A  pdb=" N   ARG D  28 " --> pdb=" O   LEU D  24 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ILE D  39 " --> pdb=" O   GLY D  35 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 61
    Processing helix  chain 'D' and resid 62 through 110
      removed outlier: 3.634A  pdb=" N   ILE D  94 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 110 through 115
    Processing helix  chain 'D' and resid 118 through 127
      removed outlier: 3.593A  pdb=" N   LEU D 125 " --> pdb=" O   SER D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 127 through 132
    Processing helix  chain 'D' and resid 133 through 139
      removed outlier: 3.648A  pdb=" N   TYR D 137 " --> pdb=" O   MET D 133 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 139 through 159
      removed outlier: 4.003A  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 164 through 172
      removed outlier: 3.549A  pdb=" N   LEU D 169 " --> pdb=" O   ALA D 165 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   THR D 172 " --> pdb=" O   ILE D 168 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 174 through 194
      removed outlier: 3.837A  pdb=" N   LEU D 178 " --> pdb=" O   PRO D 174 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLY D 186 " --> pdb=" O   LEU D 182 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASP D 189 " --> pdb=" O   MET D 185 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 194 through 203
      removed outlier: 4.218A  pdb=" N   GLY D 203 " --> pdb=" O   ALA D 199 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 203 through 210
    Processing helix  chain 'D' and resid 211 through 218
      removed outlier: 3.782A  pdb=" N   LEU D 215 " --> pdb=" O   GLY D 211 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 224 through 272
      removed outlier: 3.694A  pdb=" N   ASP D 234 " --> pdb=" O   SER D 230 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   LEU D 245 " --> pdb=" O   GLU D 241 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LEU D 248 " --> pdb=" O   ARG D 244 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   LEU D 253 " --> pdb=" O   SER D 249 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLU D 254 " --> pdb=" O   SER D 250 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 287 through 310
      removed outlier: 3.709A  pdb=" N   ALA D 293 " --> pdb=" O   ALA D 289 " (cutoff:3.500A)
      Proline residue:  D 298  - end of helix
      removed outlier: 4.002A  pdb=" N   PHE D 301 " --> pdb=" O   ALA D 297 " (cutoff:3.500A)
      Proline residue:  D 303  - end of helix
      removed outlier: 3.678A  pdb=" N   GLY D 308 " --> pdb=" O   LEU D 304 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 311 through 330
      removed outlier: 3.761A  pdb=" N   ALA D 315 " --> pdb=" O   TYR D 311 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   SER D 323 " --> pdb=" O   GLY D 319 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   THR D 326 " --> pdb=" O   ASP D 322 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 388 through 397
      removed outlier: 3.570A  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 422
    Processing helix  chain 'D' and resid 438 through 444
    Processing helix  chain 'D' and resid 451 through 462
    Processing helix  chain 'D' and resid 467 through 471
    Processing helix  chain 'D' and resid 487 through 500
    Processing helix  chain 'D' and resid 517 through 530
    Processing helix  chain 'D' and resid 566 through 573
    Processing helix  chain 'D' and resid 575 through 583
    Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 363
      removed outlier: 7.247A  pdb=" N   LYS C 357 " --> pdb=" O   GLN C 345 " (cutoff:3.500A)
      removed outlier: 4.916A  pdb=" N   GLN C 345 " --> pdb=" O   LYS C 357 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   ILE C 359 " --> pdb=" O   ASP C 343 " (cutoff:3.500A)
      removed outlier: 5.511A  pdb=" N   LEU C 341 " --> pdb=" O   LEU C 398 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   LEU C 398 " --> pdb=" O   LEU C 341 " (cutoff:3.500A)
      removed outlier: 5.485A  pdb=" N   ASP C 343 " --> pdb=" O   GLU C 396 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   GLU C 396 " --> pdb=" O   ASP C 343 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLN C 394 " --> pdb=" O   GLN C 345 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 416 through 419
      removed outlier: 6.476A  pdb=" N   SER C 417 " --> pdb=" O   LEU C 497 " (cutoff:3.500A)
      removed outlier: 8.118A  pdb=" N   ASP C 499 " --> pdb=" O   SER C 417 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   VAL C 419 " --> pdb=" O   ASP C 499 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ILE C 369 " --> pdb=" O   MET C 528 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   THR C 530 " --> pdb=" O   ILE C 369 " (cutoff:3.500A)
      removed outlier: 5.758A  pdb=" N   ILE C 371 " --> pdb=" O   THR C 530 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   HIS C 368 " --> pdb=" O   GLN C 541 " (cutoff:3.500A)
      removed outlier: 7.972A  pdb=" N   ILE C 543 " --> pdb=" O   HIS C 368 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   ALA C 370 " --> pdb=" O   ILE C 543 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   MET C 545 " --> pdb=" O   ALA C 370 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   LEU C 372 " --> pdb=" O   MET C 545 " (cutoff:3.500A)
      removed outlier: 3.641A  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: 5.860A  pdb=" N   LEU D 365 " --> pdb=" O   THR D 358 " (cutoff:3.500A)
      removed outlier: 7.268A  pdb=" N   THR D 358 " --> pdb=" O   LEU D 365 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   GLY D 367 " --> pdb=" O   PHE D 356 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   PHE D 356 " --> pdb=" O   GLY D 367 " (cutoff:3.500A)
      removed outlier: 5.482A  pdb=" N   LEU D 369 " --> pdb=" O   GLU D 354 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLU D 354 " --> pdb=" O   LEU D 369 " (cutoff:3.500A)
      removed outlier: 3.804A  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: 5.860A  pdb=" N   LEU D 365 " --> pdb=" O   THR D 358 " (cutoff:3.500A)
      removed outlier: 7.268A  pdb=" N   THR D 358 " --> pdb=" O   LEU D 365 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   GLY D 367 " --> pdb=" O   PHE D 356 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   PHE D 356 " --> pdb=" O   GLY D 367 " (cutoff:3.500A)
      removed outlier: 5.482A  pdb=" N   LEU D 369 " --> pdb=" O   GLU D 354 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLU D 354 " --> pdb=" O   LEU D 369 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 425 through 426
      removed outlier: 6.308A  pdb=" N   LEU D 507 " --> pdb=" O   LEU D 538 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   VAL D 540 " --> pdb=" O   LEU D 507 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   VAL D 380 " --> pdb=" O   TRP D 554 " (cutoff:3.500A)
      removed outlier: 7.516A  pdb=" N   MET D 556 " --> pdb=" O   VAL D 380 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   VAL D 382 " --> pdb=" O   MET D 556 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   VAL D 555 " --> pdb=" O   ILE D 562 " (cutoff:3.500A)

    542 hydrogen bonds defined for protein.
    1578 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: 1.43

  Time building geometry restraints manager: 0.85 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: 2075
        1.33 -     1.45: 1851
        1.45 -     1.57: 5242
        1.57 -     1.69: 8
        1.69 -     1.81: 55
  Bond restraints: 9231
  Sorted by residual:
  bond pdb=" C4  ATP D 602 "
       pdb=" C5  ATP D 602 "
    ideal  model  delta    sigma   weight residual
    1.388  1.469 -0.081 1.00e-02 1.00e+04 6.56e+01
  bond pdb=" C5  ATP D 602 "
       pdb=" C6  ATP D 602 "
    ideal  model  delta    sigma   weight residual
    1.409  1.476 -0.067 1.00e-02 1.00e+04 4.53e+01
  bond pdb=" O2  PO3 C 603 "
       pdb=" P   PO3 C 603 "
    ideal  model  delta    sigma   weight residual
    1.604  1.506  0.098 2.00e-02 2.50e+03 2.41e+01
  bond pdb=" O1  PO3 C 603 "
       pdb=" P   PO3 C 603 "
    ideal  model  delta    sigma   weight residual
    1.604  1.506  0.098 2.00e-02 2.50e+03 2.39e+01
  bond pdb=" O3  PO3 C 603 "
       pdb=" P   PO3 C 603 "
    ideal  model  delta    sigma   weight residual
    1.601  1.506  0.095 2.00e-02 2.50e+03 2.26e+01
  ... (remaining 9226 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.15: 12503
        4.15 -     8.29: 46
        8.29 -    12.44: 2
       12.44 -    16.59: 1
       16.59 -    20.74: 1
  Bond angle restraints: 12553
  Sorted by residual:
  angle pdb=" PB  ATP D 602 "
        pdb=" O3B ATP D 602 "
        pdb=" PG  ATP D 602 "
      ideal   model   delta    sigma   weight residual
     139.87  119.13   20.74 1.00e+00 1.00e+00 4.30e+02
  angle pdb=" PA  ATP D 602 "
        pdb=" O3A ATP D 602 "
        pdb=" PB  ATP D 602 "
      ideal   model   delta    sigma   weight residual
     136.83  121.55   15.28 1.00e+00 1.00e+00 2.34e+02
  angle pdb=" C5  ATP D 602 "
        pdb=" C4  ATP D 602 "
        pdb=" N3  ATP D 602 "
      ideal   model   delta    sigma   weight residual
     126.80  118.92    7.88 1.00e+00 1.00e+00 6.22e+01
  angle pdb=" N3  ATP D 602 "
        pdb=" C4  ATP D 602 "
        pdb=" N9  ATP D 602 "
      ideal   model   delta    sigma   weight residual
     127.04  134.87   -7.83 1.15e+00 7.59e-01 4.66e+01
  angle pdb=" N1  ATP D 602 "
        pdb=" C2  ATP D 602 "
        pdb=" N3  ATP D 602 "
      ideal   model   delta    sigma   weight residual
     128.69  123.59    5.10 1.00e+00 1.00e+00 2.60e+01
  ... (remaining 12548 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.08: 5156
       24.08 -    48.16: 327
       48.16 -    72.24: 19
       72.24 -    96.32: 14
       96.32 -   120.40: 2
  Dihedral angle restraints: 5518
    sinusoidal: 2193
      harmonic: 3325
  Sorted by residual:
  dihedral pdb=" O1B ADP C 602 "
           pdb=" O3A ADP C 602 "
           pdb=" PB  ADP C 602 "
           pdb=" PA  ADP C 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  179.60  120.40     1      2.00e+01 2.50e-03 3.61e+01
  dihedral pdb=" C5' ADP C 602 "
           pdb=" O5' ADP C 602 "
           pdb=" PA  ADP C 602 "
           pdb=" O2A ADP C 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -179.38  119.38     1      2.00e+01 2.50e-03 3.58e+01
  dihedral pdb=" C   ASP D 282 "
           pdb=" N   ASP D 282 "
           pdb=" CA  ASP D 282 "
           pdb=" CB  ASP D 282 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.62   10.02     0      2.50e+00 1.60e-01 1.61e+01
  ... (remaining 5515 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1309
       0.069 -    0.139: 135
       0.139 -    0.208: 9
       0.208 -    0.277: 3
       0.277 -    0.347: 1
  Chirality restraints: 1457
  Sorted by residual:
  chirality pdb=" CA  ASP D 282 "
            pdb=" N   ASP D 282 "
            pdb=" C   ASP D 282 "
            pdb=" CB  ASP D 282 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.00e+00
  chirality pdb=" CA  ARG C  13 "
            pdb=" N   ARG C  13 "
            pdb=" C   ARG C  13 "
            pdb=" CB  ARG C  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.67e+00
  chirality pdb=" CA  LEU D 509 "
            pdb=" N   LEU D 509 "
            pdb=" C   LEU D 509 "
            pdb=" CB  LEU D 509 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 1454 not shown)

  Planarity restraints: 1598
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR D 281 "   -0.024 2.00e-02 2.50e+03   4.99e-02 2.49e+01
        pdb=" C   TYR D 281 "    0.086 2.00e-02 2.50e+03
        pdb=" O   TYR D 281 "   -0.032 2.00e-02 2.50e+03
        pdb=" N   ASP D 282 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C 348 "   -0.042 5.00e-02 4.00e+02   6.38e-02 6.51e+00
        pdb=" N   PRO C 349 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO C 349 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO C 349 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D 159 "    0.030 5.00e-02 4.00e+02   4.57e-02 3.34e+00
        pdb=" N   PRO D 160 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO D 160 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO D 160 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1595 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 54
        2.53 -     3.12: 6708
        3.12 -     3.72: 14201
        3.72 -     4.31: 20708
        4.31 -     4.90: 34362
  Nonbonded interactions: 76033
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 390 "
            pdb="MG    MG D 601 "
     model   vdw
     1.941 2.170
  nonbonded pdb=" OE1 GLN C 421 "
            pdb="MG    MG C 601 "
     model   vdw
     2.127 2.170
  nonbonded pdb="MG    MG D 601 "
            pdb=" O1B ATP D 602 "
     model   vdw
     2.138 2.170
  nonbonded pdb=" OG  SER C 380 "
            pdb="MG    MG C 601 "
     model   vdw
     2.185 2.170
  nonbonded pdb="MG    MG D 601 "
            pdb=" O1G ATP D 602 "
     model   vdw
     2.222 2.170
  ... (remaining 76028 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:             2.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     9.610
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
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   0.098   9231  Z= 0.336
  Angle     :  0.772  20.737  12553  Z= 0.508
  Chirality :  0.046   0.347   1457
  Planarity :  0.005   0.064   1598
  Dihedral  : 15.048 120.400   3374
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.53 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.09 (0.23), residues: 1155
  helix: -1.58 (0.18), residues: 721
  sheet:  0.83 (0.71), residues: 52
  loop : -0.90 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D 193 
 TYR   0.010   0.002   TYR C   7 
 PHE   0.015   0.002   PHE C 291 
 TRP   0.015   0.002   TRP D 427 
 HIS   0.005   0.001   HIS C  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00609 ( 9231)
  covalent geometry    : angle       0.77211 (12553)
  hydrogen bonds       : bond        0.25749 (  538)
  hydrogen bonds       : angle       9.94945 ( 1578)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 178
  time to evaluate  : 0.331 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 179
  average time/residue: 0.1300
  time to fit residues: 29.9708
Evaluate side-chains
  127 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  332 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.6980
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    4.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
C 190 GLN
C 208 GLN
C 302 GLN
C 306 GLN
C 424 HIS
C 541 GLN
D  50 GLN
D 430 GLN
D 482 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.148510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.115844 restraints weight = 12015.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 1.47
r_work: 0.3167 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   9231  Z= 0.182
  Angle     :  0.649  10.798  12553  Z= 0.328
  Chirality :  0.043   0.169   1457
  Planarity :  0.005   0.053   1598
  Dihedral  :  8.583 111.425   1309
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  :  7.16 %
    Favored  : 90.92 %
  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: -0.57 (0.24), residues: 1155
  helix:  0.00 (0.19), residues: 727
  sheet:  1.01 (0.75), residues: 42
  loop : -1.09 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 560 
 TYR   0.011   0.001   TYR C   7 
 PHE   0.016   0.002   PHE C 175 
 TRP   0.023   0.002   TRP D 427 
 HIS   0.004   0.001   HIS D 542 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 9231)
  covalent geometry    : angle       0.64890 (12553)
  hydrogen bonds       : bond        0.04951 (  538)
  hydrogen bonds       : angle       5.02056 ( 1578)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 136
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7934 (tttm)
REVERT: D  154 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8405 (mp)
REVERT: D  557 GLN cc_start: 0.8692 (tt0) cc_final: 0.8308 (mt0)
REVERT: D  560 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7787 (mtm110)
  outliers start: 18
  outliers final: 5
  residues processed: 147
  average time/residue: 0.1104
  time to fit residues: 21.5055
Evaluate side-chains
  123 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   12 LYS
Chi-restraints excluded: chain C residue  556 HIS
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  230 SER
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  332 LEU
Chi-restraints excluded: chain D residue  372 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 50 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 58 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 42 optimal weight:    0.5980
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
D   6 GLN
D 194 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.148540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.113208 restraints weight = 11984.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 1.68
r_work: 0.3152 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3022 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9231  Z= 0.138
  Angle     :  0.570  10.887  12553  Z= 0.285
  Chirality :  0.041   0.155   1457
  Planarity :  0.004   0.048   1598
  Dihedral  :  8.042 102.203   1309
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 10.47 %
    Favored  : 87.93 %
  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:  0.25 (0.24), residues: 1155
  helix:  0.79 (0.19), residues: 724
  sheet:  1.12 (0.76), residues: 42
  loop : -1.05 (0.29), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 384 
 TYR   0.013   0.001   TYR C  59 
 PHE   0.015   0.002   PHE D 278 
 TRP   0.024   0.002   TRP D 427 
 HIS   0.003   0.001   HIS D 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 9231)
  covalent geometry    : angle       0.57035 (12553)
  hydrogen bonds       : bond        0.04461 (  538)
  hydrogen bonds       : angle       4.51389 ( 1578)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7891 (tttm)
REVERT: C  160 PHE cc_start: 0.8462 (t80) cc_final: 0.8048 (t80)
REVERT: C  448 GLU cc_start: 0.8623 (pp20) cc_final: 0.8237 (pp20)
REVERT: D  154 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8546 (mp)
REVERT: D  463 TRP cc_start: 0.8553 (m-90) cc_final: 0.8238 (m-90)
  outliers start: 15
  outliers final: 10
  residues processed: 131
  average time/residue: 0.1102
  time to fit residues: 19.3916
Evaluate side-chains
  119 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   12 LYS
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  401 ASP
Chi-restraints excluded: chain C residue  556 HIS
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   92 GLN
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  230 SER
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  332 LEU
Chi-restraints excluded: chain D residue  372 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 100 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   chunk 79 optimal weight:    0.7980
   chunk 107 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    1.2986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.145901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.113992 restraints weight = 12077.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 1.56
r_work: 0.3125 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071   9231  Z= 0.187
  Angle     :  0.597  12.074  12553  Z= 0.296
  Chirality :  0.043   0.152   1457
  Planarity :  0.004   0.046   1598
  Dihedral  :  7.654 100.071   1309
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 11.97 %
    Favored  : 85.79 %
  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:  0.54 (0.24), residues: 1155
  helix:  1.09 (0.20), residues: 713
  sheet:  1.33 (0.78), residues: 42
  loop : -1.05 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 313 
 TYR   0.012   0.001   TYR D  88 
 PHE   0.015   0.002   PHE C 164 
 TRP   0.027   0.002   TRP D 427 
 HIS   0.004   0.001   HIS D 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 9231)
  covalent geometry    : angle       0.59655 (12553)
  hydrogen bonds       : bond        0.04423 (  538)
  hydrogen bonds       : angle       4.42103 ( 1578)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7978 (tttm)
REVERT: C  160 PHE cc_start: 0.8432 (t80) cc_final: 0.8213 (t80)
REVERT: C  448 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8212 (pp20)
REVERT: C  500 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.6768 (mp0)
REVERT: D  154 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8623 (mp)
  outliers start: 21
  outliers final: 13
  residues processed: 135
  average time/residue: 0.1116
  time to fit residues: 20.3360
Evaluate side-chains
  122 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   12 LYS
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  401 ASP
Chi-restraints excluded: chain C residue  448 GLU
Chi-restraints excluded: chain C residue  500 GLU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   92 GLN
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  230 SER
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  332 LEU
Chi-restraints excluded: chain D residue  372 THR
Chi-restraints excluded: chain D residue  396 LEU
Chi-restraints excluded: chain D residue  547 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 95 optimal weight:    0.5980
   chunk 5 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 3 optimal weight:    0.5980
   chunk 108 optimal weight:    0.0970
   chunk 83 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 96 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
C 116 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.148760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.116447 restraints weight = 12041.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 1.48
r_work: 0.3157 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3033 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9231  Z= 0.118
  Angle     :  0.542  11.871  12553  Z= 0.268
  Chirality :  0.040   0.143   1457
  Planarity :  0.004   0.045   1598
  Dihedral  :  7.217  95.146   1309
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 14.64 %
    Favored  : 83.65 %
  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:  0.92 (0.25), residues: 1155
  helix:  1.41 (0.20), residues: 719
  sheet:  1.82 (0.79), residues: 41
  loop : -1.00 (0.29), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 384 
 TYR   0.013   0.001   TYR D  88 
 PHE   0.013   0.001   PHE D 467 
 TRP   0.026   0.002   TRP D 427 
 HIS   0.002   0.000   HIS D 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 9231)
  covalent geometry    : angle       0.54184 (12553)
  hydrogen bonds       : bond        0.03941 (  538)
  hydrogen bonds       : angle       4.18567 ( 1578)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8224 (mttt) cc_final: 0.7973 (tttm)
REVERT: C  448 GLU cc_start: 0.8431 (pp20) cc_final: 0.8193 (pp20)
REVERT: C  500 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.6831 (mp0)
  outliers start: 16
  outliers final: 11
  residues processed: 130
  average time/residue: 0.1085
  time to fit residues: 19.0963
Evaluate side-chains
  123 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  360 SER
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  401 ASP
Chi-restraints excluded: chain C residue  456 GLU
Chi-restraints excluded: chain C residue  500 GLU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue  230 SER
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  332 LEU
Chi-restraints excluded: chain D residue  372 THR
Chi-restraints excluded: chain D residue  547 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 85 optimal weight:    8.9990
   chunk 32 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 93 optimal weight:    0.0270
   chunk 64 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   overall best weight:    1.9644

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

Flipped N/Q/H residues before XYZ refinement:
C 116 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.144960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.110682 restraints weight = 12292.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 1.54
r_work: 0.3063 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.2984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.093   9231  Z= 0.245
  Angle     :  0.648  12.579  12553  Z= 0.317
  Chirality :  0.045   0.154   1457
  Planarity :  0.004   0.043   1598
  Dihedral  :  7.359  98.195   1309
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.06 %
    Favored  : 82.37 %
  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:  0.59 (0.24), residues: 1155
  helix:  1.12 (0.19), residues: 721
  sheet:  1.67 (0.83), residues: 42
  loop : -1.07 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 313 
 TYR   0.013   0.002   TYR C   7 
 PHE   0.017   0.002   PHE D 467 
 TRP   0.026   0.002   TRP D 427 
 HIS   0.005   0.001   HIS D 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00608 ( 9231)
  covalent geometry    : angle       0.64825 (12553)
  hydrogen bonds       : bond        0.04660 (  538)
  hydrogen bonds       : angle       4.42411 ( 1578)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7997 (tttm)
REVERT: C  160 PHE cc_start: 0.8471 (t80) cc_final: 0.8237 (t80)
REVERT: C  251 MET cc_start: 0.8825 (tpt) cc_final: 0.8542 (mmt)
REVERT: C  500 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7086 (mp0)
REVERT: C  534 ARG cc_start: 0.8059 (tpt90) cc_final: 0.7764 (mmm160)
  outliers start: 24
  outliers final: 16
  residues processed: 128
  average time/residue: 0.1209
  time to fit residues: 20.3948
Evaluate side-chains
  125 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   12 LYS
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  146 VAL
Chi-restraints excluded: chain C residue  164 PHE
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  360 SER
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  401 ASP
Chi-restraints excluded: chain C residue  500 GLU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue  230 SER
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  286 THR
Chi-restraints excluded: chain D residue  372 THR
Chi-restraints excluded: chain D residue  396 LEU
Chi-restraints excluded: chain D residue  427 TRP
Chi-restraints excluded: chain D residue  547 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 102 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 17 optimal weight:    0.1980
   chunk 24 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   chunk 43 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
D 542 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.147965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.114985 restraints weight = 12149.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 1.54
r_work: 0.3113 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   9231  Z= 0.131
  Angle     :  0.570  13.425  12553  Z= 0.277
  Chirality :  0.040   0.150   1457
  Planarity :  0.004   0.044   1598
  Dihedral  :  6.997  94.302   1307
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 16.03 %
    Favored  : 81.84 %
  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:  0.93 (0.25), residues: 1155
  helix:  1.42 (0.20), residues: 712
  sheet:  2.04 (0.82), residues: 41
  loop : -1.00 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 384 
 TYR   0.020   0.001   TYR C 567 
 PHE   0.016   0.001   PHE D 467 
 TRP   0.024   0.002   TRP D 427 
 HIS   0.006   0.001   HIS C 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9231)
  covalent geometry    : angle       0.56970 (12553)
  hydrogen bonds       : bond        0.04031 (  538)
  hydrogen bonds       : angle       4.20204 ( 1578)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8197 (mttt) cc_final: 0.7935 (tttm)
REVERT: C   13 ARG cc_start: 0.7897 (mmm160) cc_final: 0.7669 (mmt90)
REVERT: C   60 MET cc_start: 0.8169 (mmt) cc_final: 0.7950 (mmm)
REVERT: C  160 PHE cc_start: 0.8388 (t80) cc_final: 0.8180 (t80)
REVERT: C  500 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7035 (mp0)
  outliers start: 20
  outliers final: 13
  residues processed: 132
  average time/residue: 0.1123
  time to fit residues: 19.5725
Evaluate side-chains
  120 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  164 PHE
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  360 SER
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  500 GLU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue  230 SER
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  286 THR
Chi-restraints excluded: chain D residue  372 THR
Chi-restraints excluded: chain D residue  396 LEU
Chi-restraints excluded: chain D residue  427 TRP
Chi-restraints excluded: chain D residue  547 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
C 116 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.146707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.113166 restraints weight = 12184.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 1.52
r_work: 0.3090 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.3213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   9231  Z= 0.155
  Angle     :  0.583  13.664  12553  Z= 0.283
  Chirality :  0.041   0.142   1457
  Planarity :  0.004   0.044   1598
  Dihedral  :  6.943  94.035   1307
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 16.88 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.25), residues: 1155
  helix:  1.51 (0.20), residues: 706
  sheet:  2.02 (0.82), residues: 41
  loop : -0.97 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 384 
 TYR   0.015   0.001   TYR C 567 
 PHE   0.016   0.002   PHE D 467 
 TRP   0.024   0.002   TRP D 427 
 HIS   0.006   0.001   HIS C 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 9231)
  covalent geometry    : angle       0.58269 (12553)
  hydrogen bonds       : bond        0.04118 (  538)
  hydrogen bonds       : angle       4.16379 ( 1578)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8236 (mttt) cc_final: 0.7971 (tttm)
REVERT: C  500 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7064 (mp0)
REVERT: C  534 ARG cc_start: 0.8080 (tpt90) cc_final: 0.7795 (mmm160)
  outliers start: 19
  outliers final: 16
  residues processed: 134
  average time/residue: 0.1184
  time to fit residues: 20.8671
Evaluate side-chains
  127 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  146 VAL
Chi-restraints excluded: chain C residue  164 PHE
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  360 SER
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  500 GLU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  230 SER
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  286 THR
Chi-restraints excluded: chain D residue  332 LEU
Chi-restraints excluded: chain D residue  372 THR
Chi-restraints excluded: chain D residue  396 LEU
Chi-restraints excluded: chain D residue  427 TRP
Chi-restraints excluded: chain D residue  547 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 55 optimal weight:    0.1980
   chunk 69 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 108 optimal weight:    4.9990
   chunk 68 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 110 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
C 116 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.148097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.114857 restraints weight = 12150.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.52
r_work: 0.3119 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.3312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9231  Z= 0.130
  Angle     :  0.570  13.623  12553  Z= 0.277
  Chirality :  0.040   0.137   1457
  Planarity :  0.004   0.044   1598
  Dihedral  :  6.874  92.465   1307
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.31 %
    Favored  : 80.88 %
  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:  1.14 (0.25), residues: 1155
  helix:  1.63 (0.20), residues: 709
  sheet:  2.10 (0.82), residues: 41
  loop : -0.97 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  13 
 TYR   0.014   0.001   TYR C 567 
 PHE   0.021   0.001   PHE C 164 
 TRP   0.023   0.002   TRP D 427 
 HIS   0.007   0.001   HIS C 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 9231)
  covalent geometry    : angle       0.57027 (12553)
  hydrogen bonds       : bond        0.03925 (  538)
  hydrogen bonds       : angle       4.07930 ( 1578)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8183 (mttt) cc_final: 0.7915 (tttm)
REVERT: C   60 MET cc_start: 0.8171 (mmt) cc_final: 0.7924 (mmm)
REVERT: C  500 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7099 (mp0)
REVERT: C  534 ARG cc_start: 0.8038 (tpt90) cc_final: 0.7757 (mmm160)
  outliers start: 17
  outliers final: 12
  residues processed: 131
  average time/residue: 0.1127
  time to fit residues: 19.7423
Evaluate side-chains
  127 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  146 VAL
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  500 GLU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue  230 SER
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  286 THR
Chi-restraints excluded: chain D residue  332 LEU
Chi-restraints excluded: chain D residue  372 THR
Chi-restraints excluded: chain D residue  396 LEU
Chi-restraints excluded: chain D residue  547 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 100 optimal weight:    0.0770
   chunk 47 optimal weight:    6.9990
   chunk 102 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0570
   chunk 72 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.4656

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

Flipped N/Q/H residues before XYZ refinement:
C 116 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.149510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.116681 restraints weight = 12077.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 1.51
r_work: 0.3174 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.3423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9231  Z= 0.118
  Angle     :  0.570  14.249  12553  Z= 0.275
  Chirality :  0.040   0.163   1457
  Planarity :  0.004   0.044   1598
  Dihedral  :  6.781  90.667   1307
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 17.84 %
    Favored  : 80.77 %
  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:  1.37 (0.25), residues: 1155
  helix:  1.79 (0.20), residues: 718
  sheet:  2.18 (0.83), residues: 41
  loop : -0.89 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 384 
 TYR   0.015   0.001   TYR C 567 
 PHE   0.015   0.001   PHE D 577 
 TRP   0.024   0.002   TRP D 427 
 HIS   0.006   0.000   HIS C 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9231)
  covalent geometry    : angle       0.56996 (12553)
  hydrogen bonds       : bond        0.03779 (  538)
  hydrogen bonds       : angle       3.98742 ( 1578)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8178 (mttt) cc_final: 0.7915 (tttm)
REVERT: C   60 MET cc_start: 0.8143 (mmt) cc_final: 0.7903 (mmm)
REVERT: C  534 ARG cc_start: 0.8048 (tpt90) cc_final: 0.7799 (mmm160)
REVERT: D  198 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7704 (mt)
  outliers start: 13
  outliers final: 10
  residues processed: 128
  average time/residue: 0.1111
  time to fit residues: 19.1201
Evaluate side-chains
  123 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  230 SER
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  286 THR
Chi-restraints excluded: chain D residue  332 LEU
Chi-restraints excluded: chain D residue  372 THR
Chi-restraints excluded: chain D residue  547 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 111 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0670
   chunk 18 optimal weight:    1.9990
   chunk 91 optimal weight:    5.9990
   chunk 7 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 108 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.9324

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

Flipped N/Q/H residues before XYZ refinement:
C 116 GLN
C 553 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.148354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.115840 restraints weight = 12020.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.49
r_work: 0.3160 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.3417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   9231  Z= 0.151
  Angle     :  0.591  14.473  12553  Z= 0.284
  Chirality :  0.041   0.152   1457
  Planarity :  0.004   0.044   1598
  Dihedral  :  6.828  91.563   1307
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 18.06 %
    Favored  : 80.56 %
  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:  1.22 (0.25), residues: 1155
  helix:  1.69 (0.20), residues: 709
  sheet:  1.99 (0.85), residues: 42
  loop : -0.91 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 384 
 TYR   0.013   0.001   TYR C 567 
 PHE   0.022   0.002   PHE C 164 
 TRP   0.024   0.002   TRP D 427 
 HIS   0.005   0.001   HIS C 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 9231)
  covalent geometry    : angle       0.59116 (12553)
  hydrogen bonds       : bond        0.03991 (  538)
  hydrogen bonds       : angle       4.04394 ( 1578)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2401.78 seconds
wall clock time: 41 minutes 33.39 seconds (2493.39 seconds total)