Starting phenix.real_space_refine
on Thu Feb 13 18:42:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ze5_14684/02_2025/7ze5_14684_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ze5_14684/02_2025/7ze5_14684.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ze5_14684/02_2025/7ze5_14684.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ze5_14684/02_2025/7ze5_14684.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ze5_14684/02_2025/7ze5_14684_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ze5_14684/02_2025/7ze5_14684_neut.cif"
  }
  resolution = 2.94
  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=  -0.000 sd=   0.005
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      30      5.16       5
     C    5796      2.51       5
     N    1598      2.21       5
     O    1645      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 53 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9077
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 4421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 571, 4421
          Classifications: {'peptide': 571}
          Link IDs: {'PTRANS': 18, 'TRANS': 552}
    Chain: "D"
      Number of atoms: 4592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 588, 4592
          Classifications: {'peptide': 588}
          Link IDs: {'PTRANS': 27, 'TRANS': 560}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.90, per 1000 atoms: 0.65
  Number of scatterers: 9077
  At special positions: 0
  Unit cell: (117.18, 97.929, 102.951, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      30     16.00
     P       6     15.00
     Mg      2     11.99
     O    1645      8.00
     N    1598      7.00
     C    5796      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: 2.93
  Conformation dependent library (CDL) restraints added in 1.2 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:  2146

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 5 sheets defined
      69.6% alpha, 9.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'C' and resid 1 through 3
      No H-bonds generated for 'chain 'C' and resid 1 through 3'
    Processing helix  chain 'C' and resid 4 through 9
    Processing helix  chain 'C' and resid 10 through 13
      removed outlier: 3.690A  pdb=" N   ARG C  13 " --> pdb=" O   LEU C  10 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 10 through 13'
    Processing helix  chain 'C' and resid 14 through 50
      removed outlier: 3.593A  pdb=" N   LEU C  29 " --> pdb=" O   ALA C  25 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LEU C  36 " --> pdb=" O   SER C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 54
    Processing helix  chain 'C' and resid 59 through 101
      removed outlier: 3.532A  pdb=" N   ALA C  87 " --> pdb=" O   VAL C  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 107
      Proline residue:  C 105  - end of helix
      No H-bonds generated for 'chain 'C' and resid 102 through 107'
    Processing helix  chain 'C' and resid 110 through 114
    Processing helix  chain 'C' and resid 115 through 125
    Processing helix  chain 'C' and resid 125 through 130
      removed outlier: 3.566A  pdb=" N   LEU C 130 " --> pdb=" O   ASP C 126 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 130 through 136
      removed outlier: 3.579A  pdb=" N   TYR C 134 " --> pdb=" O   LEU C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 159
      removed outlier: 3.503A  pdb=" N   LEU C 141 " --> pdb=" O   VAL C 137 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE C 148 " --> pdb=" O   ALA C 144 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   PHE C 157 " --> pdb=" O   ILE C 153 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   LEU C 158 " --> pdb=" O   GLY C 154 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 160 through 175
    Processing helix  chain 'C' and resid 176 through 185
    Processing helix  chain 'C' and resid 185 through 209
      removed outlier: 3.526A  pdb=" N   GLY C 197 " --> pdb=" O   THR C 193 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 216
      removed outlier: 3.727A  pdb=" N   ILE C 215 " --> pdb=" O   ALA C 211 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE C 216 " --> pdb=" O   GLU C 212 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 218 through 267
      removed outlier: 3.638A  pdb=" N   SER C 267 " --> pdb=" O   LEU C 263 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 278 through 291
      removed outlier: 3.776A  pdb=" N   CYS C 286 " --> pdb=" O   LEU C 282 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   PHE C 291 " --> pdb=" O   ALA C 287 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 296 through 303
      removed outlier: 3.826A  pdb=" N   PHE C 301 " --> pdb=" O   VAL C 297 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 303 through 319
      removed outlier: 3.501A  pdb=" N   ALA C 309 " --> pdb=" O   GLY C 305 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ARG C 313 " --> pdb=" O   ALA C 309 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 378 through 386
    Processing helix  chain 'C' and resid 405 through 407
      No H-bonds generated for 'chain 'C' and resid 405 through 407'
    Processing helix  chain 'C' and resid 408 through 413
    Processing helix  chain 'C' and resid 429 through 435
    Processing helix  chain 'C' and resid 442 through 454
    Processing helix  chain 'C' and resid 455 through 460
    Processing helix  chain 'C' and resid 462 through 466
      removed outlier: 3.553A  pdb=" N   ASN C 465 " --> pdb=" O   ALA C 462 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 476 through 492
      removed outlier: 3.567A  pdb=" N   ARG C 482 " --> pdb=" O   GLY C 478 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 506 through 521
    Processing helix  chain 'C' and resid 555 through 563
    Processing helix  chain 'C' and resid 564 through 571
      removed outlier: 3.631A  pdb=" N   GLN C 568 " --> pdb=" O   GLY C 564 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 16
    Processing helix  chain 'D' and resid 17 through 19
      No H-bonds generated for 'chain 'D' and resid 17 through 19'
    Processing helix  chain 'D' and resid 20 through 54
    Processing helix  chain 'D' and resid 63 through 110
      removed outlier: 3.719A  pdb=" N   GLY D 110 " --> pdb=" O   LEU D 106 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 110 through 115
    Processing helix  chain 'D' and resid 118 through 127
    Processing helix  chain 'D' and resid 127 through 132
    Processing helix  chain 'D' and resid 133 through 139
    Processing helix  chain 'D' and resid 139 through 157
      removed outlier: 4.690A  pdb=" N   ALA D 145 " --> pdb=" O   LEU D 141 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU D 146 " --> pdb=" O   PRO D 142 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   VAL D 148 " --> pdb=" O   MET D 144 " (cutoff:3.500A)
      Proline residue:  D 151  - end of helix
      removed outlier: 3.564A  pdb=" N   ALA D 157 " --> pdb=" O   LEU D 153 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 162 through 173
      removed outlier: 3.714A  pdb=" N   ALA D 166 " --> pdb=" O   ASN D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 174 through 184
      removed outlier: 3.512A  pdb=" N   LEU D 178 " --> pdb=" O   PRO D 174 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 186 through 211
    Processing helix  chain 'D' and resid 211 through 218
      removed outlier: 3.650A  pdb=" N   LEU D 215 " --> pdb=" O   GLY D 211 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 220 through 274
      removed outlier: 3.631A  pdb=" N   LEU D 245 " --> pdb=" O   GLU D 241 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU D 273 " --> pdb=" O   GLY D 269 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 330
      removed outlier: 3.675A  pdb=" N   ALA D 297 " --> pdb=" O   ALA D 293 " (cutoff:3.500A)
      Proline residue:  D 298  - end of helix
      removed outlier: 3.757A  pdb=" N   PHE D 301 " --> pdb=" O   ALA D 297 " (cutoff:3.500A)
      Proline residue:  D 303  - end of helix
      removed outlier: 3.743A  pdb=" N   HIS D 312 " --> pdb=" O   GLY D 308 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ALA D 313 " --> pdb=" O   THR D 309 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   SER D 323 " --> pdb=" O   GLY D 319 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   LEU D 324 " --> pdb=" O   ALA D 320 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 388 through 397
    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 463 through 467
      removed outlier: 3.753A  pdb=" N   GLU D 466 " --> pdb=" O   TRP D 463 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 473 through 477
      removed outlier: 3.855A  pdb=" N   ASP D 476 " --> pdb=" O   GLN D 473 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   THR D 477 " --> pdb=" O   GLY D 474 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 473 through 477'
    Processing helix  chain 'D' and resid 487 through 502
      removed outlier: 3.565A  pdb=" N   ALA D 499 " --> pdb=" O   ALA D 495 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   ASN D 502 " --> pdb=" O   ARG D 498 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 517 through 533
      removed outlier: 3.877A  pdb=" N   ALA D 527 " --> pdb=" O   ARG D 523 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU D 533 " --> pdb=" O   ASN D 529 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 566 through 572
      removed outlier: 4.134A  pdb=" N   VAL D 572 " --> pdb=" O   ALA D 568 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 574 through 584
      removed outlier: 3.709A  pdb=" N   ALA D 578 " --> pdb=" O   GLY D 574 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   HIS D 583 " --> pdb=" O   THR D 579 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   ARG D 584 " --> pdb=" O   LEU D 580 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 363
      removed outlier: 6.749A  pdb=" N   LYS C 357 " --> pdb=" O   GLN C 345 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   GLN C 345 " --> pdb=" O   LYS C 357 " (cutoff:3.500A)
      removed outlier: 5.005A  pdb=" N   ILE C 359 " --> pdb=" O   ASP C 343 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 416 through 419
      removed outlier: 6.386A  pdb=" N   SER C 417 " --> pdb=" O   LEU C 497 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   ASP C 499 " --> pdb=" O   SER C 417 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   VAL C 419 " --> pdb=" O   ASP C 499 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   VAL C 496 " --> pdb=" O   LEU C 527 " (cutoff:3.500A)
      removed outlier: 7.400A  pdb=" N   VAL C 529 " --> pdb=" O   VAL C 496 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   LEU C 498 " --> pdb=" O   VAL C 529 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   ILE C 369 " --> pdb=" O   MET C 528 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   HIS C 368 " --> pdb=" O   GLN C 541 " (cutoff:3.500A)
      removed outlier: 7.990A  pdb=" N   ILE C 543 " --> pdb=" O   HIS C 368 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   ALA C 370 " --> pdb=" O   ILE C 543 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   MET C 545 " --> pdb=" O   ALA C 370 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   LEU C 372 " --> pdb=" O   MET C 545 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   ILE C 542 " --> pdb=" O   GLN C 553 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   GLN C 553 " --> pdb=" O   ILE C 542 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   VAL C 544 " --> pdb=" O   ILE C 551 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 364 through 373
      removed outlier: 6.643A  pdb=" N   ILE D 357 " --> pdb=" O   LEU D 365 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   GLY D 367 " --> pdb=" O   LEU D 355 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   LEU D 355 " --> pdb=" O   GLY D 367 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   LEU D 369 " --> pdb=" O   GLU D 353 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   GLU D 353 " --> pdb=" O   LEU D 369 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   PHE D 371 " --> pdb=" O   GLU D 351 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   GLU D 351 " --> pdb=" O   PHE D 371 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   SER D 401 " --> pdb=" O   THR D 358 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 364 through 373
      removed outlier: 6.643A  pdb=" N   ILE D 357 " --> pdb=" O   LEU D 365 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   GLY D 367 " --> pdb=" O   LEU D 355 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   LEU D 355 " --> pdb=" O   GLY D 367 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   LEU D 369 " --> pdb=" O   GLU D 353 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   GLU D 353 " --> pdb=" O   LEU D 369 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   PHE D 371 " --> pdb=" O   GLU D 351 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   GLU D 351 " --> pdb=" O   PHE D 371 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 425 through 428
      removed outlier: 6.914A  pdb=" N   SER D 426 " --> pdb=" O   LEU D 508 " (cutoff:3.500A)
      removed outlier: 7.933A  pdb=" N   ASP D 510 " --> pdb=" O   SER D 426 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   VAL D 428 " --> pdb=" O   ASP D 510 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   ARG D 378 " --> pdb=" O   VAL D 552 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   TRP D 554 " --> pdb=" O   ARG D 378 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   VAL D 380 " --> pdb=" O   TRP D 554 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   MET D 556 " --> pdb=" O   VAL D 380 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   VAL D 382 " --> pdb=" O   MET D 556 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   VAL D 555 " --> pdb=" O   ILE D 562 " (cutoff:3.500A)

    563 hydrogen bonds defined for protein.
    1644 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: 3.17

  Time building geometry restraints manager: 2.97 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: 2143
        1.33 -     1.45: 1811
        1.45 -     1.57: 5235
        1.57 -     1.69: 10
        1.69 -     1.81: 58
  Bond restraints: 9257
  Sorted by residual:
  bond pdb=" C4  ATP C 602 "
       pdb=" C5  ATP C 602 "
    ideal  model  delta    sigma   weight residual
    1.388  1.467 -0.079 1.00e-02 1.00e+04 6.25e+01
  bond pdb=" O3A ANP D 602 "
       pdb=" PB  ANP D 602 "
    ideal  model  delta    sigma   weight residual
    1.700  1.556  0.144 2.00e-02 2.50e+03 5.21e+01
  bond pdb=" C5  ATP C 602 "
       pdb=" C6  ATP C 602 "
    ideal  model  delta    sigma   weight residual
    1.409  1.478 -0.069 1.00e-02 1.00e+04 4.82e+01
  bond pdb=" N3B ANP D 602 "
       pdb=" PG  ANP D 602 "
    ideal  model  delta    sigma   weight residual
    1.795  1.691  0.104 2.00e-02 2.50e+03 2.68e+01
  bond pdb=" C5  ATP C 602 "
       pdb=" N7  ATP C 602 "
    ideal  model  delta    sigma   weight residual
    1.387  1.343  0.044 1.00e-02 1.00e+04 1.93e+01
  ... (remaining 9252 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.09: 12542
        4.09 -     8.17: 38
        8.17 -    12.26: 5
       12.26 -    16.34: 2
       16.34 -    20.43: 1
  Bond angle restraints: 12588
  Sorted by residual:
  angle pdb=" PB  ATP C 602 "
        pdb=" O3B ATP C 602 "
        pdb=" PG  ATP C 602 "
      ideal   model   delta    sigma   weight residual
     139.87  119.44   20.43 1.00e+00 1.00e+00 4.17e+02
  angle pdb=" PA  ATP C 602 "
        pdb=" O3A ATP C 602 "
        pdb=" PB  ATP C 602 "
      ideal   model   delta    sigma   weight residual
     136.83  121.12   15.71 1.00e+00 1.00e+00 2.47e+02
  angle pdb=" C5  ATP C 602 "
        pdb=" C4  ATP C 602 "
        pdb=" N3  ATP C 602 "
      ideal   model   delta    sigma   weight residual
     126.80  118.78    8.02 1.00e+00 1.00e+00 6.44e+01
  angle pdb=" N3  ATP C 602 "
        pdb=" C4  ATP C 602 "
        pdb=" N9  ATP C 602 "
      ideal   model   delta    sigma   weight residual
     127.04  135.02   -7.98 1.15e+00 7.59e-01 4.83e+01
  angle pdb=" N1  ATP C 602 "
        pdb=" C2  ATP C 602 "
        pdb=" N3  ATP C 602 "
      ideal   model   delta    sigma   weight residual
     128.69  123.67    5.02 1.00e+00 1.00e+00 2.52e+01
  ... (remaining 12583 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.76: 5090
       19.76 -    39.51: 372
       39.51 -    59.27: 67
       59.27 -    79.02: 26
       79.02 -    98.78: 5
  Dihedral angle restraints: 5560
    sinusoidal: 2233
      harmonic: 3327
  Sorted by residual:
  dihedral pdb=" CA  LEU D 425 "
           pdb=" C   LEU D 425 "
           pdb=" N   SER D 426 "
           pdb=" CA  SER D 426 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.30   18.70     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  LEU C 106 "
           pdb=" C   LEU C 106 "
           pdb=" N   SER C 107 "
           pdb=" CA  SER C 107 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.06  -17.94     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  THR C 530 "
           pdb=" C   THR C 530 "
           pdb=" N   HIS C 531 "
           pdb=" CA  HIS C 531 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.26   17.74     0      5.00e+00 4.00e-02 1.26e+01
  ... (remaining 5557 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1206
       0.054 -    0.107: 215
       0.107 -    0.161: 32
       0.161 -    0.215: 3
       0.215 -    0.269: 3
  Chirality restraints: 1459
  Sorted by residual:
  chirality pdb=" CB  THR C 530 "
            pdb=" CA  THR C 530 "
            pdb=" OG1 THR C 530 "
            pdb=" CG2 THR C 530 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.28    0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" C3' ANP D 602 "
            pdb=" C2' ANP D 602 "
            pdb=" C4' ANP D 602 "
            pdb=" O3' ANP D 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.61    0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" CA  ILE C 397 "
            pdb=" N   ILE C 397 "
            pdb=" C   ILE C 397 "
            pdb=" CB  ILE C 397 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 1456 not shown)

  Planarity restraints: 1602
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR C 114 "   -0.013 2.00e-02 2.50e+03   2.74e-02 7.50e+00
        pdb=" C   TYR C 114 "    0.047 2.00e-02 2.50e+03
        pdb=" O   TYR C 114 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ARG C 115 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET C 177 "    0.028 5.00e-02 4.00e+02   4.20e-02 2.82e+00
        pdb=" N   PRO C 178 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO C 178 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C 178 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C 527 "    0.007 2.00e-02 2.50e+03   1.49e-02 2.22e+00
        pdb=" C   LEU C 527 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   LEU C 527 "    0.010 2.00e-02 2.50e+03
        pdb=" N   MET C 528 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1599 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 46
        2.50 -     3.10: 6403
        3.10 -     3.70: 14192
        3.70 -     4.30: 21262
        4.30 -     4.90: 35422
  Nonbonded interactions: 77325
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN D 430 "
            pdb="MG    MG D 601 "
     model   vdw
     1.901 2.170
  nonbonded pdb=" OG  SER D 390 "
            pdb="MG    MG D 601 "
     model   vdw
     1.903 2.170
  nonbonded pdb="MG    MG D 601 "
            pdb=" O3G ANP D 602 "
     model   vdw
     1.907 2.170
  nonbonded pdb="MG    MG D 601 "
            pdb=" O2B ANP D 602 "
     model   vdw
     1.929 2.170
  nonbonded pdb=" OE1 GLN C 421 "
            pdb="MG    MG C 601 "
     model   vdw
     1.970 2.170
  ... (remaining 77320 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:             1.480
  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:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.660
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.060
  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:13.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.144   9257  Z= 0.342
  Angle     :  0.738  20.427  12588  Z= 0.476
  Chirality :  0.044   0.269   1459
  Planarity :  0.003   0.042   1602
  Dihedral  : 14.944  98.778   3414
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  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: -0.78 (0.24), residues: 1155
  helix: -0.45 (0.19), residues: 685
  sheet: -0.45 (0.64), residues: 62
  loop : -0.33 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D 427 
 HIS   0.006   0.001   HIS D 542 
 PHE   0.016   0.001   PHE C 539 
 TYR   0.016   0.001   TYR D  88 
 ARG   0.005   0.000   ARG D 238 

*********************** 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
  114 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  186 LYS cc_start: 0.8500 (tttm) cc_final: 0.8137 (ttmt)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 1.6367
  time to fit residues: 197.2044
Evaluate side-chains
  95 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 87 optimal weight:    0.3980
   chunk 48 optimal weight:    0.8980
   chunk 29 optimal weight:    0.4980
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    0.3980
   chunk 90 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 104 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
C 198 GLN
C 208 GLN
C 228 ASN
** C 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  41 GLN
D 433 GLN
D 543 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.117054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.096483 restraints weight = 11955.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 1.67
r_work: 0.2980 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8793
moved from start:          0.1368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9257  Z= 0.205
  Angle     :  0.572   7.253  12588  Z= 0.296
  Chirality :  0.040   0.175   1459
  Planarity :  0.004   0.042   1602
  Dihedral  :  9.787  89.404   1329
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  :  8.39 %
    Favored  : 89.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.05 (0.25), residues: 1155
  helix:  1.29 (0.19), residues: 702
  sheet: -0.03 (0.67), residues: 62
  loop : -0.11 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 163 
 HIS   0.004   0.001   HIS D 134 
 PHE   0.019   0.001   PHE D 467 
 TYR   0.020   0.001   TYR D  88 
 ARG   0.004   0.000   ARG C 223 

*********************** 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
  120 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
REVERT: C  186 LYS cc_start: 0.8682 (tttm) cc_final: 0.8289 (ttmt)
REVERT: C  323 GLU cc_start: 0.8253 (tt0) cc_final: 0.8052 (mt-10)
REVERT: C  394 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7559 (tm-30)
REVERT: C  457 LYS cc_start: 0.8599 (ttmm) cc_final: 0.8235 (ttpm)
REVERT: C  521 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8416 (mtp)
REVERT: D  226 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7829 (tm-30)
  outliers start: 17
  outliers final: 4
  residues processed: 109
  average time/residue: 1.5616
  time to fit residues: 180.0893
Evaluate side-chains
  101 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  520 MET
Chi-restraints excluded: chain C residue  521 MET
Chi-restraints excluded: chain D residue  226 GLU
Chi-restraints excluded: chain D residue  342 LEU
Chi-restraints excluded: chain D residue  451 SER
Chi-restraints excluded: chain D residue  465 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 100 optimal weight:    0.4980
   chunk 25 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
C 531 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.113983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.092753 restraints weight = 11939.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 1.63
r_work: 0.2860 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2728 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8789
moved from start:          0.1626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9257  Z= 0.221
  Angle     :  0.531   7.533  12588  Z= 0.270
  Chirality :  0.040   0.150   1459
  Planarity :  0.004   0.042   1602
  Dihedral  :  8.955  78.542   1329
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 10.93 %
    Favored  : 87.05 %
  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:  1.77 (0.25), residues: 1155
  helix:  1.96 (0.19), residues: 700
  sheet:  0.26 (0.68), residues: 62
  loop : -0.04 (0.32), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D  81 
 HIS   0.005   0.001   HIS D 312 
 PHE   0.018   0.001   PHE C  89 
 TYR   0.022   0.001   TYR D  88 
 ARG   0.005   0.000   ARG C 374 

*********************** 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
  124 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  171 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8363 (mp)
REVERT: C  186 LYS cc_start: 0.8634 (tttm) cc_final: 0.8303 (ttpt)
REVERT: C  323 GLU cc_start: 0.8290 (tt0) cc_final: 0.8069 (mt-10)
REVERT: C  394 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7581 (tm-30)
REVERT: C  521 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8348 (mtp)
REVERT: D   47 ARG cc_start: 0.7697 (mtp85) cc_final: 0.7496 (mtm180)
REVERT: D  115 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7734 (tt0)
REVERT: D  226 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7734 (tm-30)
REVERT: D  336 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7883 (tm-30)
REVERT: D  523 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8500 (mmt90)
  outliers start: 19
  outliers final: 3
  residues processed: 112
  average time/residue: 1.5369
  time to fit residues: 182.1770
Evaluate side-chains
  103 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  521 MET
Chi-restraints excluded: chain D residue  115 GLN
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  226 GLU
Chi-restraints excluded: chain D residue  336 GLN
Chi-restraints excluded: chain D residue  342 LEU
Chi-restraints excluded: chain D residue  523 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 105 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 98 optimal weight:    0.3980
   chunk 110 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 114 optimal weight:    6.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.3341 r_free = 0.3341 target = 0.111838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.090139 restraints weight = 11935.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 1.72
r_work: 0.2919 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2785 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8805
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9257  Z= 0.240
  Angle     :  0.533   7.499  12588  Z= 0.268
  Chirality :  0.040   0.150   1459
  Planarity :  0.004   0.046   1602
  Dihedral  :  8.012  75.080   1329
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 11.78 %
    Favored  : 85.99 %
  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:  2.04 (0.25), residues: 1155
  helix:  2.17 (0.19), residues: 702
  sheet:  0.36 (0.67), residues: 62
  loop :  0.05 (0.33), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  81 
 HIS   0.005   0.001   HIS D 312 
 PHE   0.017   0.001   PHE D 467 
 TYR   0.022   0.001   TYR D  88 
 ARG   0.009   0.000   ARG D 560 

*********************** 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
  117 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  186 LYS cc_start: 0.8611 (tttm) cc_final: 0.8289 (ttpt)
REVERT: C  394 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7525 (tm-30)
REVERT: C  521 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8344 (mtp)
REVERT: C  534 ARG cc_start: 0.8671 (ttt90) cc_final: 0.8377 (ttt-90)
REVERT: D   47 ARG cc_start: 0.7729 (mtp85) cc_final: 0.7514 (mtm180)
REVERT: D  115 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7925 (mt0)
REVERT: D  226 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7748 (tm-30)
  outliers start: 21
  outliers final: 4
  residues processed: 104
  average time/residue: 1.5910
  time to fit residues: 174.9056
Evaluate side-chains
  99 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  520 MET
Chi-restraints excluded: chain C residue  521 MET
Chi-restraints excluded: chain D residue  115 GLN
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  226 GLU
Chi-restraints excluded: chain D residue  342 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 107 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 64 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
C 512 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.114594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.092443 restraints weight = 11912.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 1.74
r_work: 0.2908 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2771 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8818
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9257  Z= 0.278
  Angle     :  0.552   8.471  12588  Z= 0.276
  Chirality :  0.041   0.226   1459
  Planarity :  0.004   0.054   1602
  Dihedral  :  7.788  78.206   1329
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 11.78 %
    Favored  : 85.67 %
  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:  2.13 (0.25), residues: 1155
  helix:  2.28 (0.19), residues: 703
  sheet:  0.41 (0.66), residues: 62
  loop :  0.02 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D  81 
 HIS   0.005   0.001   HIS D 312 
 PHE   0.018   0.001   PHE D 467 
 TYR   0.021   0.001   TYR D  88 
 ARG   0.011   0.000   ARG D 560 

*********************** 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
  115 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
REVERT: C  186 LYS cc_start: 0.8603 (tttm) cc_final: 0.8282 (ttpt)
REVERT: C  251 MET cc_start: 0.9080 (tpp) cc_final: 0.8864 (mmp)
REVERT: C  394 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7222 (tm-30)
REVERT: C  521 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8355 (mtp)
REVERT: C  534 ARG cc_start: 0.8690 (ttt90) cc_final: 0.8380 (ttt-90)
REVERT: D   47 ARG cc_start: 0.7737 (mtp85) cc_final: 0.7487 (mtm180)
REVERT: D  115 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7995 (mt0)
REVERT: D  144 MET cc_start: 0.8506 (tpt) cc_final: 0.7556 (mtm)
REVERT: D  226 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7791 (tm-30)
REVERT: D  336 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7752 (tm-30)
REVERT: D  523 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8492 (mmt90)
  outliers start: 24
  outliers final: 8
  residues processed: 104
  average time/residue: 1.5988
  time to fit residues: 175.8956
Evaluate side-chains
  101 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  359 ILE
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  520 MET
Chi-restraints excluded: chain C residue  521 MET
Chi-restraints excluded: chain D residue  115 GLN
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  226 GLU
Chi-restraints excluded: chain D residue  286 THR
Chi-restraints excluded: chain D residue  336 GLN
Chi-restraints excluded: chain D residue  342 LEU
Chi-restraints excluded: chain D residue  451 SER
Chi-restraints excluded: chain D residue  523 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 68 optimal weight:    0.7980
   chunk 28 optimal weight:    5.9990
   chunk 111 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 112 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 98 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3378 r_free = 0.3378 target = 0.114308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.092946 restraints weight = 11788.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 1.62
r_work: 0.2945 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2813 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8796
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9257  Z= 0.211
  Angle     :  0.521   7.651  12588  Z= 0.262
  Chirality :  0.040   0.206   1459
  Planarity :  0.004   0.053   1602
  Dihedral  :  7.472  79.020   1329
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.16 %
    Favored  : 84.71 %
  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:  2.29 (0.25), residues: 1155
  helix:  2.42 (0.19), residues: 702
  sheet:  0.52 (0.66), residues: 62
  loop :  0.06 (0.33), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D  81 
 HIS   0.004   0.001   HIS C 132 
 PHE   0.017   0.001   PHE C  89 
 TYR   0.020   0.001   TYR D  88 
 ARG   0.012   0.000   ARG D 560 

*********************** 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
  115 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
REVERT: C  186 LYS cc_start: 0.8550 (tttm) cc_final: 0.8277 (ttpt)
REVERT: C  394 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7241 (tm-30)
REVERT: C  521 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8339 (mtp)
REVERT: C  534 ARG cc_start: 0.8723 (ttt90) cc_final: 0.8427 (ttt-90)
REVERT: D   47 ARG cc_start: 0.7755 (mtp85) cc_final: 0.7511 (mtm180)
REVERT: D  144 MET cc_start: 0.8467 (tpt) cc_final: 0.7567 (mtm)
REVERT: D  226 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7758 (tm-30)
REVERT: D  523 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8455 (mmt90)
  outliers start: 20
  outliers final: 7
  residues processed: 105
  average time/residue: 1.6106
  time to fit residues: 178.4366
Evaluate side-chains
  96 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  520 MET
Chi-restraints excluded: chain C residue  521 MET
Chi-restraints excluded: chain D residue  226 GLU
Chi-restraints excluded: chain D residue  286 THR
Chi-restraints excluded: chain D residue  342 LEU
Chi-restraints excluded: chain D residue  523 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 72 optimal weight:    0.6980
   chunk 104 optimal weight:    0.5980
   chunk 94 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 77 optimal weight:    0.3980
   chunk 112 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3407 r_free = 0.3407 target = 0.116464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.094248 restraints weight = 11949.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 1.77
r_work: 0.2951 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2814 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8766
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9257  Z= 0.189
  Angle     :  0.512   8.469  12588  Z= 0.257
  Chirality :  0.039   0.153   1459
  Planarity :  0.004   0.060   1602
  Dihedral  :  7.317  81.226   1329
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 13.06 %
    Favored  : 84.61 %
  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:  2.45 (0.25), residues: 1155
  helix:  2.55 (0.19), residues: 704
  sheet:  0.62 (0.67), residues: 62
  loop :  0.09 (0.33), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP D 427 
 HIS   0.004   0.001   HIS D 312 
 PHE   0.017   0.001   PHE C  89 
 TYR   0.018   0.001   TYR D  88 
 ARG   0.014   0.000   ARG D 560 

*********************** 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
  113 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
REVERT: C  186 LYS cc_start: 0.8485 (tttm) cc_final: 0.8202 (ttpt)
REVERT: C  251 MET cc_start: 0.9057 (tpp) cc_final: 0.8812 (mmt)
REVERT: C  323 GLU cc_start: 0.8301 (tt0) cc_final: 0.8054 (mt-10)
REVERT: C  394 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7197 (tm-30)
REVERT: C  521 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8342 (mtp)
REVERT: C  534 ARG cc_start: 0.8702 (ttt90) cc_final: 0.8403 (ttt-90)
REVERT: D   47 ARG cc_start: 0.7738 (mtp85) cc_final: 0.7491 (mtm180)
REVERT: D  226 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7685 (tm-30)
REVERT: D  336 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7584 (tm-30)
REVERT: D  523 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8479 (mmt90)
  outliers start: 22
  outliers final: 9
  residues processed: 100
  average time/residue: 1.6617
  time to fit residues: 175.3671
Evaluate side-chains
  101 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue  149 MET
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  457 LYS
Chi-restraints excluded: chain C residue  521 MET
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  226 GLU
Chi-restraints excluded: chain D residue  336 GLN
Chi-restraints excluded: chain D residue  342 LEU
Chi-restraints excluded: chain D residue  427 TRP
Chi-restraints excluded: chain D residue  523 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   chunk 110 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 99 optimal weight:    4.9990
   overall best weight:    1.4384

-------------------------------------------------------------------------------
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 = 0.3374 r_free = 0.3374 target = 0.113933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.091635 restraints weight = 12086.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 1.76
r_work: 0.2913 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2776 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8800
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9257  Z= 0.306
  Angle     :  0.558   7.989  12588  Z= 0.280
  Chirality :  0.042   0.228   1459
  Planarity :  0.004   0.066   1602
  Dihedral  :  7.556  84.681   1329
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 14.12 %
    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:  2.28 (0.25), residues: 1155
  helix:  2.38 (0.19), residues: 711
  sheet:  0.47 (0.67), residues: 62
  loop :  0.07 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP D 427 
 HIS   0.006   0.001   HIS D 312 
 PHE   0.018   0.002   PHE D 467 
 TYR   0.019   0.001   TYR D  88 
 ARG   0.013   0.000   ARG D 560 

*********************** 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
  110 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
REVERT: C  186 LYS cc_start: 0.8565 (tttm) cc_final: 0.8240 (ttpt)
REVERT: C  394 GLN cc_start: 0.7736 (tm-30) cc_final: 0.7082 (tm-30)
REVERT: C  521 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8344 (mtt)
REVERT: D  226 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7779 (tm-30)
REVERT: D  523 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8486 (mmt90)
  outliers start: 21
  outliers final: 9
  residues processed: 101
  average time/residue: 1.5791
  time to fit residues: 168.7913
Evaluate side-chains
  98 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  359 ILE
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  457 LYS
Chi-restraints excluded: chain C residue  521 MET
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  226 GLU
Chi-restraints excluded: chain D residue  286 THR
Chi-restraints excluded: chain D residue  342 LEU
Chi-restraints excluded: chain D residue  427 TRP
Chi-restraints excluded: chain D residue  523 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 111 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3401 r_free = 0.3401 target = 0.116044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.093952 restraints weight = 11850.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 1.75
r_work: 0.2948 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2810 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8794
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9257  Z= 0.193
  Angle     :  0.511   7.872  12588  Z= 0.259
  Chirality :  0.039   0.169   1459
  Planarity :  0.004   0.065   1602
  Dihedral  :  7.323  82.064   1329
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 14.76 %
    Favored  : 83.33 %
  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:  2.50 (0.25), residues: 1155
  helix:  2.55 (0.19), residues: 711
  sheet:  0.59 (0.67), residues: 62
  loop :  0.16 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D 427 
 HIS   0.004   0.001   HIS C 132 
 PHE   0.017   0.001   PHE C  89 
 TYR   0.019   0.001   TYR D  88 
 ARG   0.014   0.000   ARG D 560 

*********************** 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
  107 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
REVERT: C  186 LYS cc_start: 0.8518 (tttm) cc_final: 0.8268 (ttpt)
REVERT: C  394 GLN cc_start: 0.7766 (tm-30) cc_final: 0.7245 (tm-30)
REVERT: D  144 MET cc_start: 0.8193 (tpt) cc_final: 0.7502 (mtm)
REVERT: D  226 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7776 (tm-30)
REVERT: D  523 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8517 (mmt90)
  outliers start: 18
  outliers final: 11
  residues processed: 98
  average time/residue: 1.6270
  time to fit residues: 168.6916
Evaluate side-chains
  98 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue  149 MET
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  359 ILE
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  457 LYS
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  226 GLU
Chi-restraints excluded: chain D residue  286 THR
Chi-restraints excluded: chain D residue  342 LEU
Chi-restraints excluded: chain D residue  427 TRP
Chi-restraints excluded: chain D residue  523 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
C 384 GLN
C 500 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.115811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.093541 restraints weight = 12014.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 1.77
r_work: 0.2943 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2807 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8802
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9257  Z= 0.212
  Angle     :  0.520   7.701  12588  Z= 0.262
  Chirality :  0.039   0.166   1459
  Planarity :  0.004   0.070   1602
  Dihedral  :  7.316  82.426   1329
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 15.29 %
    Favored  : 83.23 %
  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:  2.51 (0.25), residues: 1155
  helix:  2.56 (0.19), residues: 711
  sheet:  0.57 (0.67), residues: 62
  loop :  0.15 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 427 
 HIS   0.005   0.001   HIS D 312 
 PHE   0.017   0.001   PHE C  89 
 TYR   0.018   0.001   TYR D  88 
 ARG   0.015   0.000   ARG D 560 

********************** 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
  104 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
REVERT: C  186 LYS cc_start: 0.8519 (tttm) cc_final: 0.8251 (ttpt)
REVERT: C  323 GLU cc_start: 0.8283 (tt0) cc_final: 0.8068 (mt-10)
REVERT: C  394 GLN cc_start: 0.7769 (tm-30) cc_final: 0.7234 (tm-30)
REVERT: C  521 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8502 (mtp)
REVERT: D  144 MET cc_start: 0.8171 (tpt) cc_final: 0.7491 (mtm)
REVERT: D  226 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7797 (tm-30)
  outliers start: 14
  outliers final: 9
  residues processed: 98
  average time/residue: 1.6228
  time to fit residues: 167.9996
Evaluate side-chains
  96 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  359 ILE
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  453 VAL
Chi-restraints excluded: chain C residue  457 LYS
Chi-restraints excluded: chain C residue  521 MET
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  226 GLU
Chi-restraints excluded: chain D residue  286 THR
Chi-restraints excluded: chain D residue  342 LEU
Chi-restraints excluded: chain D residue  427 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0570
   chunk 14 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 10 optimal weight:    0.3980
   chunk 42 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.6298

-------------------------------------------------------------------------------
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 = 0.3410 r_free = 0.3410 target = 0.116726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.094660 restraints weight = 11923.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 1.74
r_work: 0.2946 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2811 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8774
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9257  Z= 0.183
  Angle     :  0.506   7.636  12588  Z= 0.256
  Chirality :  0.039   0.153   1459
  Planarity :  0.004   0.068   1602
  Dihedral  :  7.191  83.774   1329
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 15.71 %
    Favored  : 83.12 %
  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:  2.60 (0.25), residues: 1155
  helix:  2.63 (0.19), residues: 710
  sheet:  0.64 (0.67), residues: 62
  loop :  0.19 (0.33), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 427 
 HIS   0.004   0.001   HIS D 312 
 PHE   0.017   0.001   PHE C  89 
 TYR   0.017   0.001   TYR D  88 
 ARG   0.015   0.000   ARG D 560 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6072.16 seconds
wall clock time: 107 minutes 51.24 seconds (6471.24 seconds total)