Starting phenix.real_space_refine
on Sun Jul 27 09:30:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zda_14639/07_2025/7zda_14639_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zda_14639/07_2025/7zda_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_14639/07_2025/7zda_14639.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zda_14639/07_2025/7zda_14639.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zda_14639/07_2025/7zda_14639_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zda_14639/07_2025/7zda_14639_neut.cif"
  }
  resolution = 3.17
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1}
          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: 5.59, per 1000 atoms: 0.62
  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: 2.46
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.87
  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: 2.48

  Time building geometry restraints manager: 2.85 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:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.170
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.590
-------------------------------------------------------------------------------
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 : 8.77
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.015   0.002   TRP D 427 
 HIS   0.005   0.001   HIS C  14 
 PHE   0.015   0.002   PHE C 291 
 TYR   0.010   0.002   TYR C   7 
 ARG   0.011   0.000   ARG D 193 

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

*********************** 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  : 0.930 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 179
  average time/residue: 0.3009
  time to fit residues: 69.0833
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  : 1.005 
-------------------------------------------------------------------------------
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 97 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0980
   chunk 34 optimal weight:    0.8980
   chunk 54 optimal weight:    6.9990
   chunk 67 optimal weight:    0.7980
   chunk 104 optimal weight:    3.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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
C 553 GLN
D  50 GLN
D 430 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.150058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.117697 restraints weight = 11921.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 1.46
r_work: 0.3195 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9231  Z= 0.150
  Angle     :  0.626  10.516  12553  Z= 0.319
  Chirality :  0.041   0.171   1457
  Planarity :  0.005   0.053   1598
  Dihedral  :  8.564 111.987   1309
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  7.26 %
    Favored  : 91.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.24), residues: 1155
  helix:  0.06 (0.19), residues: 727
  sheet:  1.07 (0.75), residues: 42
  loop : -1.03 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D 427 
 HIS   0.004   0.001   HIS D 542 
 PHE   0.019   0.002   PHE C 145 
 TYR   0.010   0.001   TYR C   7 
 ARG   0.003   0.000   ARG D 560 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05028 (  538)
  hydrogen bonds       : angle       5.03300 ( 1578)
  covalent geometry    : bond        0.00335 ( 9231)
  covalent geometry    : angle       0.62631 (12553)

*********************** 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
  155 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7933 (tttm)
REVERT: D  154 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8409 (mp)
REVERT: D  557 GLN cc_start: 0.8638 (tt0) cc_final: 0.8284 (mt0)
REVERT: D  560 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7812 (mtm110)
  outliers start: 16
  outliers final: 5
  residues processed: 147
  average time/residue: 0.2574
  time to fit residues: 50.4815
Evaluate side-chains
  127 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 120
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
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 28 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   chunk 59 optimal weight:    0.4980
   chunk 38 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 44 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.7380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.149590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.117904 restraints weight = 11912.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 1.44
r_work: 0.3119 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9231  Z= 0.143
  Angle     :  0.574  11.058  12553  Z= 0.288
  Chirality :  0.041   0.155   1457
  Planarity :  0.004   0.048   1598
  Dihedral  :  8.036 103.199   1309
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  9.94 %
    Favored  : 88.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.24), residues: 1155
  helix:  0.79 (0.19), residues: 723
  sheet:  1.14 (0.75), residues: 42
  loop : -1.02 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP D 427 
 HIS   0.004   0.001   HIS D 542 
 PHE   0.015   0.002   PHE D 278 
 TYR   0.012   0.001   TYR C  59 
 ARG   0.005   0.000   ARG D  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04490 (  538)
  hydrogen bonds       : angle       4.54335 ( 1578)
  covalent geometry    : bond        0.00332 ( 9231)
  covalent geometry    : angle       0.57410 (12553)

*********************** 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  : 0.934 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7944 (tttm)
REVERT: C  160 PHE cc_start: 0.8467 (t80) cc_final: 0.8043 (t80)
REVERT: C  262 MET cc_start: 0.8986 (mmp) cc_final: 0.8679 (mmp)
REVERT: C  448 GLU cc_start: 0.8501 (pp20) cc_final: 0.8151 (pp20)
REVERT: D   11 ARG cc_start: 0.8082 (mtm-85) cc_final: 0.7752 (mmt180)
REVERT: D  154 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8558 (mp)
  outliers start: 15
  outliers final: 8
  residues processed: 132
  average time/residue: 0.2620
  time to fit residues: 46.4090
Evaluate side-chains
  118 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   12 LYS
Chi-restraints excluded: chain C residue  241 SER
Chi-restraints excluded: chain C residue  372 LEU
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  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 65 optimal weight:    1.9990
   chunk 90 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 29 optimal weight:    0.0770
   chunk 112 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 76 optimal weight:    0.7980
   chunk 83 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
D  89 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.149181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.114660 restraints weight = 11918.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 1.57
r_work: 0.3169 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9231  Z= 0.130
  Angle     :  0.552  11.554  12553  Z= 0.274
  Chirality :  0.040   0.155   1457
  Planarity :  0.004   0.045   1598
  Dihedral  :  7.528  98.654   1309
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.54 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.25), residues: 1155
  helix:  1.23 (0.20), residues: 723
  sheet:  1.39 (0.76), residues: 42
  loop : -0.95 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP D 427 
 HIS   0.003   0.001   HIS D 134 
 PHE   0.013   0.002   PHE C 164 
 TYR   0.010   0.001   TYR D  88 
 ARG   0.003   0.000   ARG D 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04115 (  538)
  hydrogen bonds       : angle       4.32955 ( 1578)
  covalent geometry    : bond        0.00302 ( 9231)
  covalent geometry    : angle       0.55194 (12553)

*********************** 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
  143 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 1.425 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7926 (tttm)
REVERT: C  448 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8206 (pp20)
REVERT: D  154 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8622 (mp)
REVERT: D  547 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8616 (mp)
  outliers start: 15
  outliers final: 7
  residues processed: 138
  average time/residue: 0.2841
  time to fit residues: 53.5592
Evaluate side-chains
  117 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   12 LYS
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  448 GLU
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 35 optimal weight:    7.9990
   chunk 84 optimal weight:    6.9990
   chunk 9 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 80 optimal weight:    3.9990
   chunk 107 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
D   6 GLN
D 482 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.147245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.115009 restraints weight = 11976.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 1.58
r_work: 0.3138 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3014 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   9231  Z= 0.162
  Angle     :  0.578  13.194  12553  Z= 0.285
  Chirality :  0.042   0.146   1457
  Planarity :  0.004   0.044   1598
  Dihedral  :  7.285  97.247   1309
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 12.61 %
    Favored  : 85.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.24), residues: 1155
  helix:  1.34 (0.20), residues: 717
  sheet:  1.58 (0.80), residues: 42
  loop : -0.93 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP D 427 
 HIS   0.004   0.001   HIS D 134 
 PHE   0.012   0.002   PHE D 467 
 TYR   0.012   0.001   TYR C  59 
 ARG   0.002   0.000   ARG C 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04218 (  538)
  hydrogen bonds       : angle       4.28011 ( 1578)
  covalent geometry    : bond        0.00393 ( 9231)
  covalent geometry    : angle       0.57802 (12553)

*********************** 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
  137 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 1.997 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7985 (tttm)
REVERT: C  500 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.6686 (mp0)
REVERT: D  154 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8652 (mp)
  outliers start: 20
  outliers final: 12
  residues processed: 132
  average time/residue: 0.4332
  time to fit residues: 78.5935
Evaluate side-chains
  122 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 2.203 
-------------------------------------------------------------------------------
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  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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 114 optimal weight:    0.7980
   chunk 54 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   chunk 57 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 110 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 98 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3712 r_free = 0.3712 target = 0.148221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.113324 restraints weight = 11967.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 1.64
r_work: 0.3110 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.3010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   9231  Z= 0.144
  Angle     :  0.562  12.839  12553  Z= 0.275
  Chirality :  0.041   0.153   1457
  Planarity :  0.004   0.043   1598
  Dihedral  :  7.120  94.814   1309
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.25), residues: 1155
  helix:  1.47 (0.20), residues: 723
  sheet:  1.80 (0.82), residues: 42
  loop : -0.95 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP D 427 
 HIS   0.006   0.001   HIS C 531 
 PHE   0.014   0.002   PHE C 164 
 TYR   0.012   0.001   TYR D  88 
 ARG   0.006   0.000   ARG D 193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04048 (  538)
  hydrogen bonds       : angle       4.17517 ( 1578)
  covalent geometry    : bond        0.00344 ( 9231)
  covalent geometry    : angle       0.56228 (12553)

*********************** 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
  137 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7909 (tttm)
REVERT: C  500 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.6771 (mp0)
  outliers start: 19
  outliers final: 13
  residues processed: 131
  average time/residue: 0.2517
  time to fit residues: 45.2430
Evaluate side-chains
  127 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 1.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   12 LYS
Chi-restraints excluded: chain C residue  146 VAL
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  185 MET
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  396 LEU
Chi-restraints excluded: chain D residue  508 LEU
Chi-restraints excluded: chain D residue  540 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 108 optimal weight:    0.0000
   chunk 56 optimal weight:    5.9990
   chunk 114 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 50 optimal weight:    0.2980
   overall best weight:    0.7786

-------------------------------------------------------------------------------
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 = 0.3707 r_free = 0.3707 target = 0.148347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.114789 restraints weight = 12140.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 1.53
r_work: 0.3115 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.3131

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= 0.136
  Angle     :  0.563  13.699  12553  Z= 0.273
  Chirality :  0.041   0.151   1457
  Planarity :  0.004   0.043   1598
  Dihedral  :  7.030  93.439   1309
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 14.85 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.25), residues: 1155
  helix:  1.64 (0.20), residues: 717
  sheet:  2.16 (0.81), residues: 41
  loop : -0.92 (0.29), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP D 427 
 HIS   0.006   0.001   HIS C 531 
 PHE   0.018   0.001   PHE C 164 
 TYR   0.020   0.001   TYR C 567 
 ARG   0.004   0.000   ARG D 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03961 (  538)
  hydrogen bonds       : angle       4.11350 ( 1578)
  covalent geometry    : bond        0.00325 ( 9231)
  covalent geometry    : angle       0.56297 (12553)

*********************** 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
  142 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7938 (tttm)
REVERT: C   60 MET cc_start: 0.8119 (mmt) cc_final: 0.7919 (mmm)
REVERT: C  500 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.6830 (mp0)
  outliers start: 22
  outliers final: 14
  residues processed: 137
  average time/residue: 0.2610
  time to fit residues: 47.4650
Evaluate side-chains
  127 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
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  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  332 LEU
Chi-restraints excluded: chain D residue  372 THR
Chi-restraints excluded: chain D residue  396 LEU
Chi-restraints excluded: chain D residue  540 VAL
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 26 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 107 optimal weight:    0.0980
   chunk 96 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 98 optimal weight:    6.9990
   chunk 108 optimal weight:    0.3980
   chunk 89 optimal weight:    0.6980
   chunk 74 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0770
   overall best weight:    0.3738

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

Flipped N/Q/H residues before XYZ refinement:
C 116 GLN
D 280 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.150532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.118780 restraints weight = 12278.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 1.48
r_work: 0.3197 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.3309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   9231  Z= 0.110
  Angle     :  0.548  13.989  12553  Z= 0.265
  Chirality :  0.039   0.143   1457
  Planarity :  0.004   0.043   1598
  Dihedral  :  6.921  90.999   1309
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 16.13 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.25), residues: 1155
  helix:  1.87 (0.20), residues: 718
  sheet:  2.27 (0.81), residues: 41
  loop : -0.81 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP D 427 
 HIS   0.006   0.001   HIS C 531 
 PHE   0.016   0.001   PHE C 164 
 TYR   0.015   0.001   TYR C 567 
 ARG   0.006   0.000   ARG D 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03702 (  538)
  hydrogen bonds       : angle       3.97545 ( 1578)
  covalent geometry    : bond        0.00244 ( 9231)
  covalent geometry    : angle       0.54849 (12553)

*********************** 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
  133 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8151 (mttt) cc_final: 0.7893 (tttm)
REVERT: C   60 MET cc_start: 0.8152 (mmt) cc_final: 0.7941 (mmm)
REVERT: C  500 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.6778 (mp0)
REVERT: D  563 GLU cc_start: 0.8028 (tt0) cc_final: 0.7666 (tt0)
  outliers start: 17
  outliers final: 13
  residues processed: 129
  average time/residue: 0.2346
  time to fit residues: 41.1100
Evaluate side-chains
  126 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
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  185 MET
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  540 VAL
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 32 optimal weight:    1.9990
   chunk 85 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 81 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 105 optimal weight:    4.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3722 r_free = 0.3722 target = 0.148667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.116857 restraints weight = 12090.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.46
r_work: 0.3167 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.3309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9231  Z= 0.144
  Angle     :  0.575  13.774  12553  Z= 0.278
  Chirality :  0.041   0.138   1457
  Planarity :  0.004   0.042   1598
  Dihedral  :  6.936  92.167   1309
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 16.45 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.25), residues: 1155
  helix:  1.82 (0.20), residues: 718
  sheet:  2.32 (0.82), residues: 41
  loop : -0.84 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP D 550 
 HIS   0.005   0.001   HIS C 531 
 PHE   0.020   0.001   PHE C 164 
 TYR   0.013   0.001   TYR C 567 
 ARG   0.006   0.000   ARG D 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03930 (  538)
  hydrogen bonds       : angle       4.01219 ( 1578)
  covalent geometry    : bond        0.00348 ( 9231)
  covalent geometry    : angle       0.57507 (12553)

*********************** 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
  136 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8209 (mttt) cc_final: 0.7943 (tttm)
REVERT: C  500 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.6983 (mp0)
REVERT: C  534 ARG cc_start: 0.7984 (tpt90) cc_final: 0.7750 (mmm160)
REVERT: D  563 GLU cc_start: 0.8076 (tt0) cc_final: 0.7872 (tt0)
  outliers start: 19
  outliers final: 15
  residues processed: 131
  average time/residue: 0.2585
  time to fit residues: 45.4308
Evaluate side-chains
  130 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 1.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  500 GLU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue  185 MET
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  508 LEU
Chi-restraints excluded: chain D residue  540 VAL
Chi-restraints excluded: chain D residue  547 LEU
Chi-restraints excluded: chain D residue  570 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 91 optimal weight:    5.9990
   chunk 68 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 55 optimal weight:   10.0000
   chunk 94 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3724 r_free = 0.3724 target = 0.148727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.115331 restraints weight = 12246.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 1.54
r_work: 0.3166 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.3367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9231  Z= 0.139
  Angle     :  0.580  14.411  12553  Z= 0.279
  Chirality :  0.041   0.164   1457
  Planarity :  0.004   0.042   1598
  Dihedral  :  6.929  92.183   1309
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 16.24 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.25), residues: 1155
  helix:  1.87 (0.20), residues: 712
  sheet:  2.34 (0.82), residues: 41
  loop : -0.84 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP D 550 
 HIS   0.005   0.001   HIS C 531 
 PHE   0.020   0.001   PHE C 164 
 TYR   0.016   0.001   TYR D 402 
 ARG   0.006   0.000   ARG D 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03922 (  538)
  hydrogen bonds       : angle       4.00729 ( 1578)
  covalent geometry    : bond        0.00332 ( 9231)
  covalent geometry    : angle       0.58017 (12553)

********************** 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
  129 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8200 (mttt) cc_final: 0.7940 (tttm)
REVERT: C   60 MET cc_start: 0.8241 (mmt) cc_final: 0.8035 (mmm)
REVERT: C  500 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7076 (mp0)
  outliers start: 17
  outliers final: 15
  residues processed: 124
  average time/residue: 0.2502
  time to fit residues: 41.7175
Evaluate side-chains
  124 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  500 GLU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue  185 MET
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  508 LEU
Chi-restraints excluded: chain D residue  540 VAL
Chi-restraints excluded: chain D residue  547 LEU
Chi-restraints excluded: chain D residue  570 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0770
   chunk 60 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 110 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 10 optimal weight:    0.2980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.4938

-------------------------------------------------------------------------------
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 = 0.3737 r_free = 0.3737 target = 0.149925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.118239 restraints weight = 12161.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 1.47
r_work: 0.3186 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.3460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9231  Z= 0.120
  Angle     :  0.570  14.436  12553  Z= 0.275
  Chirality :  0.040   0.172   1457
  Planarity :  0.004   0.042   1598
  Dihedral  :  6.895  91.347   1309
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 16.35 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.25), residues: 1155
  helix:  1.94 (0.20), residues: 714
  sheet:  2.35 (0.81), residues: 41
  loop : -0.84 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP D 550 
 HIS   0.005   0.001   HIS C 531 
 PHE   0.023   0.001   PHE C 160 
 TYR   0.016   0.001   TYR D 402 
 ARG   0.006   0.000   ARG D 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03780 (  538)
  hydrogen bonds       : angle       3.95027 ( 1578)
  covalent geometry    : bond        0.00276 ( 9231)
  covalent geometry    : angle       0.56965 (12553)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5843.52 seconds
wall clock time: 104 minutes 26.32 seconds (6266.32 seconds total)