Starting phenix.real_space_refine
on Wed Mar  4 02:40:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6rah_4775/03_2026/6rah_4775.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6rah_4775/03_2026/6rah_4775.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6rah_4775/03_2026/6rah_4775.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6rah_4775/03_2026/6rah_4775.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6rah_4775/03_2026/6rah_4775.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6rah_4775/03_2026/6rah_4775.map"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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      25      5.16       5
     C    6549      2.51       5
     N    1792      2.21       5
     O    1787      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10161
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 586, 4690
          Classifications: {'peptide': 586}
          Link IDs: {'PTRANS': 24, 'TRANS': 561}
    Chain: "B"
      Number of atoms: 4506
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 570, 4499
          Classifications: {'peptide': 570}
          Link IDs: {'PTRANS': 18, 'TRANS': 551}
      Conformer: "B"
        Number of residues, atoms: 570, 4499
          Classifications: {'peptide': 570}
          Link IDs: {'PTRANS': 18, 'TRANS': 551}
          bond proxies already assigned to first conformer: 4579
    Chain: "C"
      Number of atoms: 897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 897
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 6, 'TRANS': 114}
    Chain: "A"
      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: "B"
      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: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.99, per 1000 atoms: 0.29
  Number of scatterers: 10161
  At special positions: 0
  Unit cell: (103.392, 85.083, 155.088, 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      25     16.00
     P       6     15.00
     Mg      2     11.99
     O    1787      8.00
     N    1792      7.00
     C    6549      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  50 " - pdb=" SG  CYS C 108 " distance=2.07

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 700.9 milliseconds
  

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2338

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 6 sheets defined
      65.2% alpha, 11.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 23
      removed outlier: 3.983A  pdb=" N   TYR A  21 " --> pdb=" O   ARG A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 45
    Processing helix  chain 'A' and resid 45 through 59
    Processing helix  chain 'A' and resid 65 through 120
    Processing helix  chain 'A' and resid 121 through 128
      removed outlier: 3.804A  pdb=" N   TYR A 125 " --> pdb=" O   HIS A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 138
    Processing helix  chain 'A' and resid 140 through 151
      removed outlier: 4.435A  pdb=" N   ILE A 144 " --> pdb=" O   ASP A 140 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ASN A 145 " --> pdb=" O   VAL A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 173
      removed outlier: 3.789A  pdb=" N   PHE A 171 " --> pdb=" O   GLY A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 222
      removed outlier: 3.835A  pdb=" N   VAL A 179 " --> pdb=" O   LYS A 175 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   VAL A 180 " --> pdb=" O   LEU A 176 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL A 183 " --> pdb=" O   VAL A 179 " (cutoff:3.500A)
      Proline residue:  A 185  - end of helix
      removed outlier: 3.521A  pdb=" N   LEU A 196 " --> pdb=" O   THR A 192 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLY A 197 " --> pdb=" O   TRP A 193 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ALA A 210 " --> pdb=" O   ARG A 206 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ARG A 211 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 230
      removed outlier: 3.663A  pdb=" N   LEU A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 283
      removed outlier: 3.553A  pdb=" N   ARG A 241 " --> pdb=" O   GLU A 237 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU A 242 " --> pdb=" O   LYS A 238 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ILE A 253 " --> pdb=" O   ALA A 249 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   PHE A 261 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      Proline residue:  A 262  - end of helix
      removed outlier: 3.687A  pdb=" N   ASP A 269 " --> pdb=" O   GLY A 265 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   GLY A 281 " --> pdb=" O   TYR A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 332
      removed outlier: 3.692A  pdb=" N   ASP A 298 " --> pdb=" O   VAL A 294 " (cutoff:3.500A)
      Proline residue:  A 306  - end of helix
      removed outlier: 3.977A  pdb=" N   ASP A 312 " --> pdb=" O   GLN A 308 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ARG A 326 " --> pdb=" O   ALA A 322 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   VAL A 330 " --> pdb=" O   ARG A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 407
    Processing helix  chain 'A' and resid 425 through 427
      No H-bonds generated for 'chain 'A' and resid 425 through 427'
    Processing helix  chain 'A' and resid 428 through 435
      removed outlier: 3.683A  pdb=" N   HIS A 435 " --> pdb=" O   GLU A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 455
    Processing helix  chain 'A' and resid 462 through 474
      removed outlier: 3.503A  pdb=" N   VAL A 466 " --> pdb=" O   PRO A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 481
    Processing helix  chain 'A' and resid 484 through 488
    Processing helix  chain 'A' and resid 498 through 513
    Processing helix  chain 'A' and resid 529 through 544
    Processing helix  chain 'A' and resid 578 through 586
    Processing helix  chain 'A' and resid 586 through 594
      removed outlier: 3.724A  pdb=" N   ALA A 590 " --> pdb=" O   GLY A 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 19
      Proline residue:  B  15  - end of helix
    Processing helix  chain 'B' and resid 20 through 55
      Proline residue:  B  42  - end of helix
    Processing helix  chain 'B' and resid 57 through 103
    Processing helix  chain 'B' and resid 106 through 113
      removed outlier: 3.567A  pdb=" N   TYR B 110 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 133
      removed outlier: 3.805A  pdb=" N   ASP B 125 " --> pdb=" O   ARG B 121 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   LEU B 126 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 158
    Processing helix  chain 'B' and resid 158 through 167
      removed outlier: 3.528A  pdb=" N   ALA B 162 " --> pdb=" O   ASN B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 207
      removed outlier: 3.587A  pdb=" N   ARG B 177 " --> pdb=" O   PHE B 173 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   PHE B 178 " --> pdb=" O   LEU B 174 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LEU B 179 " --> pdb=" O   ALA B 175 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU B 182 " --> pdb=" O   PHE B 178 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ASP B 184 " --> pdb=" O   LEU B 180 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ARG B 196 " --> pdb=" O   GLU B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 214
    Processing helix  chain 'B' and resid 216 through 264
      removed outlier: 3.605A  pdb=" N   VAL B 241 " --> pdb=" O   ALA B 237 " (cutoff:3.500A)
      Proline residue:  B 244  - end of helix
      removed outlier: 4.333A  pdb=" N   LEU B 249 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   GLY B 250 " --> pdb=" O   HIS B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 264 through 269
      removed outlier: 3.636A  pdb=" N   VAL B 268 " --> pdb=" O   GLY B 264 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   VAL B 269 " --> pdb=" O   GLY B 265 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 264 through 269'
    Processing helix  chain 'B' and resid 274 through 317
      removed outlier: 4.554A  pdb=" N   TRP B 290 " --> pdb=" O   ALA B 286 " (cutoff:3.500A)
      Proline residue:  B 291  - end of helix
      removed outlier: 4.032A  pdb=" N   GLY B 296 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   TRP B 297 " --> pdb=" O   LEU B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 383
    Processing helix  chain 'B' and resid 406 through 413
    Processing helix  chain 'B' and resid 427 through 433
    Processing helix  chain 'B' and resid 440 through 451
    Processing helix  chain 'B' and resid 453 through 458
    Processing helix  chain 'B' and resid 462 through 466
    Processing helix  chain 'B' and resid 476 through 491
      removed outlier: 4.243A  pdb=" N   LYS B 491 " --> pdb=" O   ARG B 487 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 518
    Processing helix  chain 'B' and resid 532 through 537
    Processing helix  chain 'B' and resid 555 through 562
    Processing helix  chain 'B' and resid 564 through 573
      removed outlier: 3.511A  pdb=" N   GLN B 573 " --> pdb=" O   MET B 569 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 30
      removed outlier: 3.560A  pdb=" N   LEU C  29 " --> pdb=" O   GLY C  26 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   ASP C  30 " --> pdb=" O   SER C  27 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 26 through 30'
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 4.086A  pdb=" N   THR C  91 " --> pdb=" O   PRO C  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 374 through 383
      removed outlier: 6.347A  pdb=" N   LEU A 360 " --> pdb=" O   VAL A 375 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   LYS A 377 " --> pdb=" O   VAL A 358 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   VAL A 358 " --> pdb=" O   LYS A 377 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   VAL A 379 " --> pdb=" O   ARG A 356 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   ARG A 356 " --> pdb=" O   VAL A 379 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   PHE A 381 " --> pdb=" O   GLU A 354 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   GLU A 354 " --> pdb=" O   PHE A 381 " (cutoff:3.500A)
      removed outlier: 5.577A  pdb=" N   PHE A 355 " --> pdb=" O   PHE A 418 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   PHE A 418 " --> pdb=" O   PHE A 355 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   ASP A 357 " --> pdb=" O   CYS A 416 " (cutoff:3.500A)
      removed outlier: 5.001A  pdb=" N   CYS A 416 " --> pdb=" O   ASP A 357 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439
      removed outlier: 6.611A  pdb=" N   GLY A 437 " --> pdb=" O   ILE A 520 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   ASP A 522 " --> pdb=" O   GLY A 437 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   VAL A 439 " --> pdb=" O   ASP A 522 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   LYS A 388 " --> pdb=" O   ARG A 564 " (cutoff:3.500A)
      removed outlier: 7.848A  pdb=" N   LEU A 566 " --> pdb=" O   LYS A 388 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   ALA A 390 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   PHE A 568 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   VAL A 392 " --> pdb=" O   PHE A 568 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLU A 575 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ARG A 569 " --> pdb=" O   LEU A 573 " (cutoff:3.500A)
      removed outlier: 5.124A  pdb=" N   LEU A 573 " --> pdb=" O   ARG A 569 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 351 through 361
      removed outlier: 6.384A  pdb=" N   LEU B 353 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   LYS B 347 " --> pdb=" O   LEU B 353 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   ARG B 355 " --> pdb=" O   GLY B 345 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   GLY B 345 " --> pdb=" O   ARG B 355 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   LEU B 357 " --> pdb=" O   GLY B 343 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLY B 343 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   VAL B 344 " --> pdb=" O   GLU B 392 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   GLU B 392 " --> pdb=" O   VAL B 344 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 414 through 417
      removed outlier: 6.459A  pdb=" N   THR B 366 " --> pdb=" O   TRP B 541 " (cutoff:3.500A)
      removed outlier: 7.758A  pdb=" N   ILE B 543 " --> pdb=" O   THR B 366 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   GLY B 368 " --> pdb=" O   ILE B 543 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   LEU B 545 " --> pdb=" O   GLY B 368 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   THR B 370 " --> pdb=" O   LEU B 545 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLU B 552 " --> pdb=" O   VAL B 544 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   ASP B 546 " --> pdb=" O   ILE B 550 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   ILE B 550 " --> pdb=" O   ASP B 546 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ALA C 101 " --> pdb=" O   VAL C 109 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 7
      removed outlier: 3.563A  pdb=" N   THR C  78 " --> pdb=" O   ASP C  73 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ASP C  73 " --> pdb=" O   THR C  78 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 12
      removed outlier: 5.675A  pdb=" N   ARG C  38 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 5.378A  pdb=" N   GLY C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)

    649 hydrogen bonds defined for protein.
    1907 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: 2.00

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1602
        1.29 -     1.42: 2713
        1.42 -     1.55: 5982
        1.55 -     1.68: 29
        1.68 -     1.82: 45
  Bond restraints: 10371
  Sorted by residual:
  bond pdb=" N   HIS B 111 "
       pdb=" CA BHIS B 111 "
    ideal  model  delta    sigma   weight residual
    1.459  1.647 -0.187 1.21e-02 6.83e+03 2.40e+02
  bond pdb=" C4  ATP B 601 "
       pdb=" C5  ATP B 601 "
    ideal  model  delta    sigma   weight residual
    1.388  1.471 -0.083 1.00e-02 1.00e+04 6.97e+01
  bond pdb=" N   PRO C 110 "
       pdb=" CD  PRO C 110 "
    ideal  model  delta    sigma   weight residual
    1.473  1.358  0.115 1.40e-02 5.10e+03 6.71e+01
  bond pdb=" C4  ATP A 701 "
       pdb=" C5  ATP A 701 "
    ideal  model  delta    sigma   weight residual
    1.388  1.466 -0.078 1.00e-02 1.00e+04 6.08e+01
  bond pdb=" N   PRO C  88 "
       pdb=" CD  PRO C  88 "
    ideal  model  delta    sigma   weight residual
    1.473  1.375  0.098 1.40e-02 5.10e+03 4.87e+01
  ... (remaining 10366 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.76: 13585
        3.76 -     7.52: 417
        7.52 -    11.28: 62
       11.28 -    15.03: 8
       15.03 -    18.79: 3
  Bond angle restraints: 14075
  Sorted by residual:
  angle pdb=" PB  ATP A 701 "
        pdb=" O3B ATP A 701 "
        pdb=" PG  ATP A 701 "
      ideal   model   delta    sigma   weight residual
     139.87  121.08   18.79 1.00e+00 1.00e+00 3.53e+02
  angle pdb=" PB  ATP B 601 "
        pdb=" O3B ATP B 601 "
        pdb=" PG  ATP B 601 "
      ideal   model   delta    sigma   weight residual
     139.87  124.23   15.64 1.00e+00 1.00e+00 2.45e+02
  angle pdb=" N   ALA C  28 "
        pdb=" CA  ALA C  28 "
        pdb=" C   ALA C  28 "
      ideal   model   delta    sigma   weight residual
     113.21  131.11  -17.90 1.15e+00 7.56e-01 2.42e+02
  angle pdb=" PA  ATP B 601 "
        pdb=" O3A ATP B 601 "
        pdb=" PB  ATP B 601 "
      ideal   model   delta    sigma   weight residual
     136.83  121.95   14.88 1.00e+00 1.00e+00 2.21e+02
  angle pdb=" PA  ATP A 701 "
        pdb=" O3A ATP A 701 "
        pdb=" PB  ATP A 701 "
      ideal   model   delta    sigma   weight residual
     136.83  123.70   13.13 1.00e+00 1.00e+00 1.73e+02
  ... (remaining 14070 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.25: 5882
       16.25 -    32.50: 229
       32.50 -    48.75: 55
       48.75 -    65.00: 18
       65.00 -    81.25: 9
  Dihedral angle restraints: 6193
    sinusoidal: 2539
      harmonic: 3654
  Sorted by residual:
  dihedral pdb=" C   VAL A  59 "
           pdb=" N   VAL A  59 "
           pdb=" CA  VAL A  59 "
           pdb=" CB  VAL A  59 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -137.97   15.97     0      2.50e+00 1.60e-01 4.08e+01
  dihedral pdb=" N   VAL C  99 "
           pdb=" C   VAL C  99 "
           pdb=" CA  VAL C  99 "
           pdb=" CB  VAL C  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  109.91   13.49     0      2.50e+00 1.60e-01 2.91e+01
  dihedral pdb=" CA  GLY A 151 "
           pdb=" C   GLY A 151 "
           pdb=" N   LEU A 152 "
           pdb=" CA  LEU A 152 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.09  -26.91     0      5.00e+00 4.00e-02 2.90e+01
  ... (remaining 6190 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 1298
       0.096 -    0.193: 214
       0.193 -    0.289: 62
       0.289 -    0.385: 24
       0.385 -    0.482: 6
  Chirality restraints: 1604
  Sorted by residual:
  chirality pdb=" CA  ILE A  54 "
            pdb=" N   ILE A  54 "
            pdb=" C   ILE A  54 "
            pdb=" CB  ILE A  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.92   -0.48 2.00e-01 2.50e+01 5.80e+00
  chirality pdb=" CA  VAL C  99 "
            pdb=" N   VAL C  99 "
            pdb=" C   VAL C  99 "
            pdb=" CB  VAL C  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.92   -0.48 2.00e-01 2.50e+01 5.79e+00
  chirality pdb=" CA  VAL C 109 "
            pdb=" N   VAL C 109 "
            pdb=" C   VAL C 109 "
            pdb=" CB  VAL C 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.88   -0.44 2.00e-01 2.50e+01 4.80e+00
  ... (remaining 1601 not shown)

  Planarity restraints: 1778
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 226 "   -0.020 2.00e-02 2.50e+03   4.03e-02 1.62e+01
        pdb=" C   ASP B 226 "    0.070 2.00e-02 2.50e+03
        pdb=" O   ASP B 226 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   LEU B 227 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A  69 "   -0.019 2.00e-02 2.50e+03   3.89e-02 1.51e+01
        pdb=" C   ARG A  69 "    0.067 2.00e-02 2.50e+03
        pdb=" O   ARG A  69 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   PHE A  70 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 223 "   -0.021 2.00e-02 2.50e+03   2.12e-02 1.12e+01
        pdb=" CG  TRP B 223 "    0.055 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 223 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 223 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 223 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 223 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 223 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 223 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 223 "   -0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 223 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1775 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 63
        2.60 -     3.17: 8040
        3.17 -     3.75: 15536
        3.75 -     4.32: 22067
        4.32 -     4.90: 36913
  Nonbonded interactions: 82619
  Sorted by model distance:
  nonbonded pdb="MG    MG A 702 "
            pdb=" O   HOH A 802 "
     model   vdw
     2.022 2.170
  nonbonded pdb=" OG1 THR A 400 "
            pdb="MG    MG A 702 "
     model   vdw
     2.047 2.170
  nonbonded pdb=" O2B ATP B 601 "
            pdb="MG    MG B 602 "
     model   vdw
     2.094 2.170
  nonbonded pdb=" O2G ATP A 701 "
            pdb="MG    MG A 702 "
     model   vdw
     2.102 2.170
  nonbonded pdb=" O2B ATP A 701 "
            pdb="MG    MG A 702 "
     model   vdw
     2.110 2.170
  ... (remaining 82614 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=0.50 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:             1.490
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.870
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.040
  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:8.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
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      :  0.008   0.187  10373  Z= 0.568
  Angle     :  1.575  44.635  14079  Z= 1.096
  Chirality :  0.091   0.482   1604
  Planarity :  0.007   0.060   1778
  Dihedral  : 10.599  81.253   3849
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.12 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Cbeta Deviations :  0.77 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.51 (0.20), residues: 1272
  helix: -1.58 (0.15), residues: 778
  sheet: -0.29 (0.43), residues: 127
  loop : -1.92 (0.27), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.026   0.001   ARG B  88 
 TYR   0.019   0.002   TYR A 299 
 PHE   0.038   0.003   PHE A 229 
 TRP   0.055   0.003   TRP B 223 
 HIS   0.008   0.002   HIS A 554 

Details of bonding type rmsd
  covalent geometry    : bond        0.00813 (10371)
  covalent geometry    : angle       1.52933 (14075)
  SS BOND              : bond        0.02729 (    2)
  SS BOND              : angle      22.38824 (    4)
  hydrogen bonds       : bond        0.18035 (  649)
  hydrogen bonds       : angle       6.47260 ( 1907)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7570 (mtm110)
REVERT: A  259 LEU cc_start: 0.8379 (tt) cc_final: 0.8174 (tp)
REVERT: A  467 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7681 (mt-10)
REVERT: A  477 GLU cc_start: 0.7534 (pt0) cc_final: 0.7120 (pt0)
REVERT: A  534 LYS cc_start: 0.8332 (tttm) cc_final: 0.8128 (ttmt)
REVERT: A  537 GLN cc_start: 0.7706 (mt0) cc_final: 0.7496 (mt0)
REVERT: A  558 THR cc_start: 0.8439 (m) cc_final: 0.8143 (m)
REVERT: B   50 ASP cc_start: 0.7870 (m-30) cc_final: 0.7661 (m-30)
REVERT: B   63 LEU cc_start: 0.8027 (mt) cc_final: 0.7797 (mt)
REVERT: B  164 TYR cc_start: 0.7160 (m-10) cc_final: 0.6876 (m-10)
REVERT: B  184 ASP cc_start: 0.8204 (t0) cc_final: 0.7986 (t0)
REVERT: B  299 MET cc_start: 0.7626 (mtm) cc_final: 0.7249 (mtt)
REVERT: B  481 GLN cc_start: 0.8438 (mt0) cc_final: 0.8221 (mt0)
REVERT: B  510 GLU cc_start: 0.7519 (tt0) cc_final: 0.7090 (tt0)
REVERT: B  568 GLU cc_start: 0.7921 (tp30) cc_final: 0.7559 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 252
  average time/residue: 0.8093
  time to fit residues: 214.4415
Evaluate side-chains
  178 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    0.6980
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 123 optimal weight:    7.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 454 HIS
B 524 GLN
B 573 GLN
C  57 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.143244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.108626 restraints weight = 24689.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 2.39
r_work: 0.3080 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2888
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2888
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10373  Z= 0.160
  Angle     :  0.617   7.893  14079  Z= 0.321
  Chirality :  0.041   0.150   1604
  Planarity :  0.005   0.035   1778
  Dihedral  :  7.175  83.973   1501
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 12.33 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.22), residues: 1272
  helix:  0.46 (0.18), residues: 792
  sheet:  0.11 (0.43), residues: 129
  loop : -1.20 (0.30), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 512 
 TYR   0.014   0.001   TYR A 427 
 PHE   0.024   0.002   PHE B  36 
 TRP   0.028   0.002   TRP B 223 
 HIS   0.005   0.001   HIS A 554 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (10371)
  covalent geometry    : angle       0.61702 (14075)
  SS BOND              : bond        0.00292 (    2)
  SS BOND              : angle       1.03140 (    4)
  hydrogen bonds       : bond        0.05235 (  649)
  hydrogen bonds       : angle       4.30929 ( 1907)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 190
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A   99 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8268 (mt0)
REVERT: A  183 VAL cc_start: 0.8461 (OUTLIER) cc_final: 0.8222 (p)
REVERT: A  334 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7779 (tp30)
REVERT: A  354 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8225 (tt0)
REVERT: A  425 ARG cc_start: 0.8628 (mtm-85) cc_final: 0.8310 (mtp85)
REVERT: A  477 GLU cc_start: 0.8211 (pt0) cc_final: 0.7761 (pt0)
REVERT: A  481 ARG cc_start: 0.8572 (mtt-85) cc_final: 0.8159 (mtt-85)
REVERT: A  534 LYS cc_start: 0.8517 (tttm) cc_final: 0.8276 (ttmt)
REVERT: B  164 TYR cc_start: 0.7668 (m-10) cc_final: 0.7429 (m-10)
REVERT: B  185 ARG cc_start: 0.8532 (ttt-90) cc_final: 0.8307 (mtp85)
REVERT: B  189 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8128 (mt-10)
REVERT: B  274 SER cc_start: 0.6841 (t) cc_final: 0.6420 (p)
REVERT: B  299 MET cc_start: 0.8450 (mtm) cc_final: 0.8022 (mtt)
REVERT: B  338 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7615 (mt-10)
REVERT: B  524 GLN cc_start: 0.8906 (pt0) cc_final: 0.8677 (pt0)
REVERT: B  532 ARG cc_start: 0.8192 (mtm180) cc_final: 0.7972 (mtm180)
REVERT: B  549 ARG cc_start: 0.8502 (pmm-80) cc_final: 0.8136 (ptm-80)
REVERT: B  568 GLU cc_start: 0.8265 (tp30) cc_final: 0.8043 (tp30)
REVERT: C   80 HIS cc_start: 0.6501 (m-70) cc_final: 0.6254 (m-70)
REVERT: C   98 THR cc_start: 0.8135 (p) cc_final: 0.7793 (p)
REVERT: C  107 ARG cc_start: 0.8485 (tpp80) cc_final: 0.7516 (tpt90)
  outliers start: 27
  outliers final: 6
  residues processed: 202
  average time/residue: 0.7369
  time to fit residues: 157.1705
Evaluate side-chains
  178 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 167
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 GLN
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  365 LYS
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  585 LYS
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain C residue   93 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 115 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 104 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 81 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
A 537 GLN
C  57 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.139652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.104732 restraints weight = 16728.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 2.18
r_work: 0.3062 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2858
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2858
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.3194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10373  Z= 0.159
  Angle     :  0.581   8.698  14079  Z= 0.298
  Chirality :  0.041   0.141   1604
  Planarity :  0.004   0.040   1778
  Dihedral  :  6.851  85.220   1501
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 13.96 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.23), residues: 1272
  helix:  1.26 (0.18), residues: 794
  sheet:  0.35 (0.44), residues: 129
  loop : -0.91 (0.31), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 512 
 TYR   0.013   0.001   TYR A 427 
 PHE   0.022   0.002   PHE B  36 
 TRP   0.025   0.002   TRP B 223 
 HIS   0.005   0.001   HIS B 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (10371)
  covalent geometry    : angle       0.58072 (14075)
  SS BOND              : bond        0.00396 (    2)
  SS BOND              : angle       0.67884 (    4)
  hydrogen bonds       : bond        0.05010 (  649)
  hydrogen bonds       : angle       4.03382 ( 1907)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 181
  time to evaluate  : 0.416 
Fit side-chains
REVERT: A   72 LEU cc_start: 0.7699 (mm) cc_final: 0.7405 (OUTLIER)
REVERT: A   94 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8260 (tt0)
REVERT: A  127 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7398 (mpp-170)
REVERT: A  199 ARG cc_start: 0.8144 (ttp-170) cc_final: 0.7356 (tpp80)
REVERT: A  334 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7787 (tp30)
REVERT: A  354 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8106 (tt0)
REVERT: A  356 ARG cc_start: 0.8546 (mtp180) cc_final: 0.6845 (ptt90)
REVERT: A  425 ARG cc_start: 0.8739 (mtm-85) cc_final: 0.8257 (mtt90)
REVERT: A  477 GLU cc_start: 0.8156 (pt0) cc_final: 0.7849 (pt0)
REVERT: A  481 ARG cc_start: 0.8541 (mtt-85) cc_final: 0.8296 (mtt-85)
REVERT: A  534 LYS cc_start: 0.8626 (tttm) cc_final: 0.8366 (ttmt)
REVERT: B  164 TYR cc_start: 0.7733 (m-10) cc_final: 0.7486 (m-10)
REVERT: B  189 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8125 (mt-10)
REVERT: B  274 SER cc_start: 0.6747 (t) cc_final: 0.6341 (p)
REVERT: B  481 GLN cc_start: 0.9136 (mt0) cc_final: 0.8786 (mt0)
REVERT: B  549 ARG cc_start: 0.8502 (pmm-80) cc_final: 0.8196 (ptm-80)
REVERT: B  568 GLU cc_start: 0.8247 (tp30) cc_final: 0.8032 (tp30)
REVERT: C  107 ARG cc_start: 0.8323 (tpp80) cc_final: 0.7406 (tpt90)
  outliers start: 27
  outliers final: 14
  residues processed: 199
  average time/residue: 0.7607
  time to fit residues: 159.4968
Evaluate side-chains
  183 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 167
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  365 LYS
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  578 SER
Chi-restraints excluded: chain A residue  585 LYS
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain C residue   93 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 122 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 123 optimal weight:    7.9990
   chunk 83 optimal weight:    4.9990
   chunk 109 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 537 GLN
B 191 GLN
** C  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.138304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.103363 restraints weight = 14773.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 2.09
r_work: 0.3049 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2887
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2887 r_free = 0.2887    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2887 r_free = 0.2887    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2887
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.3547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10373  Z= 0.173
  Angle     :  0.596   9.313  14079  Z= 0.301
  Chirality :  0.041   0.139   1604
  Planarity :  0.004   0.039   1778
  Dihedral  :  6.957  84.082   1501
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 14.34 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.23), residues: 1272
  helix:  1.40 (0.18), residues: 807
  sheet:  0.57 (0.44), residues: 129
  loop : -0.85 (0.32), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 185 
 TYR   0.017   0.001   TYR A 541 
 PHE   0.022   0.002   PHE B  36 
 TRP   0.028   0.002   TRP A  52 
 HIS   0.004   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (10371)
  covalent geometry    : angle       0.59578 (14075)
  SS BOND              : bond        0.00060 (    2)
  SS BOND              : angle       0.36350 (    4)
  hydrogen bonds       : bond        0.05060 (  649)
  hydrogen bonds       : angle       4.01349 ( 1907)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 182
  time to evaluate  : 0.400 
Fit side-chains
REVERT: A   72 LEU cc_start: 0.7909 (mm) cc_final: 0.7521 (mt)
REVERT: A   94 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8309 (tt0)
REVERT: A  127 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7417 (mpp-170)
REVERT: A  199 ARG cc_start: 0.8284 (ttp-170) cc_final: 0.7312 (tpp80)
REVERT: A  334 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7777 (tp30)
REVERT: A  356 ARG cc_start: 0.8674 (mtp180) cc_final: 0.6805 (ptt90)
REVERT: A  371 GLU cc_start: 0.8065 (tp30) cc_final: 0.7830 (tp30)
REVERT: A  477 GLU cc_start: 0.8123 (pt0) cc_final: 0.7853 (pt0)
REVERT: A  534 LYS cc_start: 0.8484 (tttm) cc_final: 0.8209 (ttmt)
REVERT: A  576 GLU cc_start: 0.7913 (tt0) cc_final: 0.7642 (tt0)
REVERT: B   35 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7651 (mp)
REVERT: B  164 TYR cc_start: 0.7781 (m-10) cc_final: 0.7523 (m-10)
REVERT: B  177 ARG cc_start: 0.7907 (mmm160) cc_final: 0.7494 (mtp-110)
REVERT: B  267 MET cc_start: 0.6672 (mmm) cc_final: 0.6066 (mmm)
REVERT: B  274 SER cc_start: 0.6795 (t) cc_final: 0.6342 (p)
REVERT: B  481 GLN cc_start: 0.9047 (mt0) cc_final: 0.8684 (mt0)
REVERT: B  549 ARG cc_start: 0.8471 (pmm-80) cc_final: 0.8159 (ptm-80)
REVERT: B  568 GLU cc_start: 0.8244 (tp30) cc_final: 0.8023 (tp30)
REVERT: C   65 LYS cc_start: 0.8697 (ttpp) cc_final: 0.8381 (ttpt)
REVERT: C   98 THR cc_start: 0.8198 (p) cc_final: 0.7908 (p)
REVERT: C  107 ARG cc_start: 0.8184 (tpp80) cc_final: 0.7325 (tpt90)
  outliers start: 32
  outliers final: 13
  residues processed: 200
  average time/residue: 0.7531
  time to fit residues: 158.7746
Evaluate side-chains
  181 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 165
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  365 LYS
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  585 LYS
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain C residue   93 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 22 optimal weight:    0.5980
   chunk 83 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   chunk 75 optimal weight:    0.0170
   chunk 109 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 120 optimal weight:    0.6980
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
A 537 GLN
B 303 GLN
B 538 HIS
C  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.140343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.105177 restraints weight = 15953.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 2.18
r_work: 0.3074 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2933
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2933 r_free = 0.2933    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2933 r_free = 0.2933    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2933
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.3739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10373  Z= 0.129
  Angle     :  0.545   9.248  14079  Z= 0.276
  Chirality :  0.039   0.138   1604
  Planarity :  0.004   0.049   1778
  Dihedral  :  6.418  87.388   1501
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 15.30 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.23), residues: 1272
  helix:  1.74 (0.18), residues: 802
  sheet:  0.65 (0.44), residues: 129
  loop : -0.68 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG B 185 
 TYR   0.014   0.001   TYR A 541 
 PHE   0.024   0.001   PHE B  36 
 TRP   0.020   0.001   TRP B 223 
 HIS   0.004   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (10371)
  covalent geometry    : angle       0.54472 (14075)
  SS BOND              : bond        0.00063 (    2)
  SS BOND              : angle       0.26571 (    4)
  hydrogen bonds       : bond        0.04440 (  649)
  hydrogen bonds       : angle       3.84944 ( 1907)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 178
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 LEU cc_start: 0.7819 (mm) cc_final: 0.7429 (mt)
REVERT: A   94 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8290 (tt0)
REVERT: A  127 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7287 (mpp-170)
REVERT: A  199 ARG cc_start: 0.8363 (ttp-170) cc_final: 0.7284 (tpp80)
REVERT: A  305 GLN cc_start: 0.8191 (mm110) cc_final: 0.7973 (mp10)
REVERT: A  356 ARG cc_start: 0.8687 (mtp180) cc_final: 0.6866 (ptt90)
REVERT: A  371 GLU cc_start: 0.8099 (tp30) cc_final: 0.7852 (tp30)
REVERT: A  464 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7746 (mp0)
REVERT: A  477 GLU cc_start: 0.8105 (pt0) cc_final: 0.7888 (pt0)
REVERT: A  525 THR cc_start: 0.8809 (p) cc_final: 0.8470 (p)
REVERT: A  534 LYS cc_start: 0.8445 (tttm) cc_final: 0.8215 (ttmt)
REVERT: A  555 ARG cc_start: 0.7675 (mtm180) cc_final: 0.7439 (mtm180)
REVERT: B   35 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7504 (mp)
REVERT: B  164 TYR cc_start: 0.7798 (m-10) cc_final: 0.7519 (m-10)
REVERT: B  177 ARG cc_start: 0.7906 (mmm160) cc_final: 0.7375 (mtp-110)
REVERT: B  181 ARG cc_start: 0.8029 (ptp90) cc_final: 0.7817 (mtm-85)
REVERT: B  267 MET cc_start: 0.6942 (mmm) cc_final: 0.6419 (mmm)
REVERT: B  481 GLN cc_start: 0.9078 (mt0) cc_final: 0.8711 (mt0)
REVERT: B  549 ARG cc_start: 0.8585 (pmm-80) cc_final: 0.8173 (ptm-80)
REVERT: C   65 LYS cc_start: 0.8707 (ttpp) cc_final: 0.8399 (ttpt)
REVERT: C  103 LEU cc_start: 0.7812 (mp) cc_final: 0.7603 (mp)
REVERT: C  107 ARG cc_start: 0.8167 (tpp80) cc_final: 0.7309 (tpt90)
  outliers start: 20
  outliers final: 11
  residues processed: 191
  average time/residue: 0.7373
  time to fit residues: 148.7542
Evaluate side-chains
  179 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 165
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  464 GLU
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  585 LYS
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   93 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0370
   chunk 25 optimal weight:    1.9990
   chunk 122 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.7060

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

Flipped N/Q/H residues before XYZ refinement:
C  57 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.138870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.106382 restraints weight = 19669.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 2.06
r_work: 0.3060 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2853
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2853
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.3826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10373  Z= 0.144
  Angle     :  0.557   9.368  14079  Z= 0.281
  Chirality :  0.039   0.147   1604
  Planarity :  0.004   0.063   1778
  Dihedral  :  6.514  88.842   1501
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 15.30 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.23), residues: 1272
  helix:  1.80 (0.18), residues: 802
  sheet:  0.75 (0.44), residues: 129
  loop : -0.58 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 560 
 TYR   0.014   0.001   TYR A 541 
 PHE   0.023   0.001   PHE B  36 
 TRP   0.018   0.001   TRP B 223 
 HIS   0.004   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (10371)
  covalent geometry    : angle       0.55709 (14075)
  SS BOND              : bond        0.00063 (    2)
  SS BOND              : angle       0.11591 (    4)
  hydrogen bonds       : bond        0.04619 (  649)
  hydrogen bonds       : angle       3.85791 ( 1907)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 171
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8308 (tt0)
REVERT: A  127 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7350 (mpp-170)
REVERT: A  199 ARG cc_start: 0.8348 (ttp-170) cc_final: 0.7351 (tpp80)
REVERT: A  305 GLN cc_start: 0.8217 (mm110) cc_final: 0.7997 (mp10)
REVERT: A  354 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8039 (tt0)
REVERT: A  356 ARG cc_start: 0.8704 (mtp180) cc_final: 0.6891 (ptt90)
REVERT: A  371 GLU cc_start: 0.8151 (tp30) cc_final: 0.7865 (mp0)
REVERT: A  464 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7790 (mp0)
REVERT: A  477 GLU cc_start: 0.8119 (pt0) cc_final: 0.7865 (pt0)
REVERT: A  525 THR cc_start: 0.8838 (p) cc_final: 0.8502 (p)
REVERT: A  534 LYS cc_start: 0.8462 (tttm) cc_final: 0.8221 (ttmt)
REVERT: A  555 ARG cc_start: 0.7726 (mtm180) cc_final: 0.7501 (mtm180)
REVERT: B   35 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7487 (mp)
REVERT: B  164 TYR cc_start: 0.7795 (m-10) cc_final: 0.7544 (m-10)
REVERT: B  177 ARG cc_start: 0.7930 (mmm160) cc_final: 0.7447 (mtp-110)
REVERT: B  481 GLN cc_start: 0.9090 (mt0) cc_final: 0.8723 (mt0)
REVERT: B  549 ARG cc_start: 0.8604 (pmm-80) cc_final: 0.8216 (ptm-80)
REVERT: C   65 LYS cc_start: 0.8722 (ttpp) cc_final: 0.8417 (ttpt)
REVERT: C   83 MET cc_start: 0.6703 (mtm) cc_final: 0.6331 (mtm)
REVERT: C  107 ARG cc_start: 0.8180 (tpp80) cc_final: 0.7317 (tpt90)
  outliers start: 27
  outliers final: 15
  residues processed: 189
  average time/residue: 0.7503
  time to fit residues: 149.6285
Evaluate side-chains
  186 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 167
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  464 GLU
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  585 LYS
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  569 MET
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   93 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 90 optimal weight:    0.0070
   chunk 1 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.8004

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

Flipped N/Q/H residues before XYZ refinement:
B 282 ASN
C  57 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.138080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.105669 restraints weight = 19593.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 2.05
r_work: 0.3049 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2824
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2824
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.3950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10373  Z= 0.152
  Angle     :  0.582  12.291  14079  Z= 0.290
  Chirality :  0.040   0.138   1604
  Planarity :  0.004   0.053   1778
  Dihedral  :  6.606  87.984   1501
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 15.30 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.64 (0.23), residues: 1272
  helix:  1.81 (0.18), residues: 806
  sheet:  0.89 (0.45), residues: 124
  loop : -0.52 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 547 
 TYR   0.013   0.001   TYR A 541 
 PHE   0.023   0.002   PHE B  36 
 TRP   0.018   0.001   TRP B 223 
 HIS   0.004   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (10371)
  covalent geometry    : angle       0.58257 (14075)
  SS BOND              : bond        0.00105 (    2)
  SS BOND              : angle       0.10275 (    4)
  hydrogen bonds       : bond        0.04713 (  649)
  hydrogen bonds       : angle       3.87017 ( 1907)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 173
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 LEU cc_start: 0.7820 (mm) cc_final: 0.7466 (mt)
REVERT: A   94 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8352 (tt0)
REVERT: A  127 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7410 (mpp-170)
REVERT: A  199 ARG cc_start: 0.8340 (ttp-170) cc_final: 0.7401 (tpp80)
REVERT: A  305 GLN cc_start: 0.8268 (mm110) cc_final: 0.8047 (mp10)
REVERT: A  354 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8057 (tt0)
REVERT: A  356 ARG cc_start: 0.8691 (mtp180) cc_final: 0.6914 (ptt90)
REVERT: A  371 GLU cc_start: 0.8155 (tp30) cc_final: 0.7837 (tp30)
REVERT: A  464 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7822 (mp0)
REVERT: A  525 THR cc_start: 0.8871 (p) cc_final: 0.8551 (p)
REVERT: A  534 LYS cc_start: 0.8571 (tttm) cc_final: 0.8322 (ttmt)
REVERT: A  555 ARG cc_start: 0.7736 (mtm180) cc_final: 0.7531 (mtm180)
REVERT: A  576 GLU cc_start: 0.7872 (tt0) cc_final: 0.7660 (tt0)
REVERT: B   35 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7479 (mp)
REVERT: B  164 TYR cc_start: 0.7815 (m-10) cc_final: 0.7585 (m-10)
REVERT: B  177 ARG cc_start: 0.7972 (mmm160) cc_final: 0.7555 (mtp-110)
REVERT: B  248 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7133 (tt)
REVERT: B  267 MET cc_start: 0.6944 (mmm) cc_final: 0.5981 (mmm)
REVERT: B  481 GLN cc_start: 0.9113 (mt0) cc_final: 0.8748 (mt0)
REVERT: B  549 ARG cc_start: 0.8586 (pmm-80) cc_final: 0.8262 (ptm-80)
REVERT: C   65 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8426 (ttpt)
REVERT: C   83 MET cc_start: 0.6744 (mtm) cc_final: 0.6370 (mtm)
REVERT: C  107 ARG cc_start: 0.8220 (tpp80) cc_final: 0.7397 (tpt90)
  outliers start: 29
  outliers final: 17
  residues processed: 191
  average time/residue: 0.7612
  time to fit residues: 153.5282
Evaluate side-chains
  193 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 171
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  464 GLU
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  578 SER
Chi-restraints excluded: chain A residue  585 LYS
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  569 MET
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   93 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 115 optimal weight:    2.9990
   chunk 99 optimal weight:    0.2980
   chunk 24 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0020
   chunk 82 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 70 optimal weight:    0.5980
   chunk 73 optimal weight:    0.5980
   chunk 80 optimal weight:    0.5980
   chunk 48 optimal weight:    3.9990
   overall best weight:    0.4188

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

Flipped N/Q/H residues before XYZ refinement:
C  80 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.140411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.106215 restraints weight = 14329.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 2.05
r_work: 0.3088 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2915
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2915
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.4044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10373  Z= 0.120
  Angle     :  0.569  11.908  14079  Z= 0.280
  Chirality :  0.038   0.138   1604
  Planarity :  0.004   0.056   1778
  Dihedral  :  6.147  87.372   1501
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.25 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.91 (0.24), residues: 1272
  helix:  2.00 (0.18), residues: 801
  sheet:  1.03 (0.46), residues: 124
  loop : -0.35 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.000   ARG A 547 
 TYR   0.013   0.001   TYR B 302 
 PHE   0.026   0.001   PHE B  36 
 TRP   0.019   0.001   TRP C  36 
 HIS   0.003   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (10371)
  covalent geometry    : angle       0.56956 (14075)
  SS BOND              : bond        0.00115 (    2)
  SS BOND              : angle       0.13737 (    4)
  hydrogen bonds       : bond        0.04209 (  649)
  hydrogen bonds       : angle       3.73761 ( 1907)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 172
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A   72 LEU cc_start: 0.7752 (mm) cc_final: 0.7428 (mt)
REVERT: A   94 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8184 (tt0)
REVERT: A  127 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8252 (mmt90)
REVERT: A  199 ARG cc_start: 0.8237 (ttp-170) cc_final: 0.7170 (tpp80)
REVERT: A  305 GLN cc_start: 0.8059 (mm110) cc_final: 0.7840 (mp10)
REVERT: A  354 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7824 (tp30)
REVERT: A  356 ARG cc_start: 0.8678 (mtp180) cc_final: 0.6841 (ptt90)
REVERT: A  371 GLU cc_start: 0.8134 (tp30) cc_final: 0.7732 (tp30)
REVERT: A  442 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7225 (tm-30)
REVERT: A  464 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7746 (mp0)
REVERT: A  525 THR cc_start: 0.8841 (p) cc_final: 0.8524 (p)
REVERT: A  534 LYS cc_start: 0.8414 (tttm) cc_final: 0.8158 (ttmt)
REVERT: A  585 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.6867 (ptmm)
REVERT: B   11 ARG cc_start: 0.8150 (ptp-170) cc_final: 0.7826 (ptp-110)
REVERT: B  132 MET cc_start: 0.8767 (ttp) cc_final: 0.8516 (ttp)
REVERT: B  164 TYR cc_start: 0.7807 (m-10) cc_final: 0.7548 (m-10)
REVERT: B  267 MET cc_start: 0.6875 (mmm) cc_final: 0.5955 (mmm)
REVERT: B  549 ARG cc_start: 0.8505 (pmm-80) cc_final: 0.8128 (ptm-80)
REVERT: C   65 LYS cc_start: 0.8729 (ttpp) cc_final: 0.8432 (ttpt)
REVERT: C   83 MET cc_start: 0.6638 (mtm) cc_final: 0.6230 (mtm)
REVERT: C  103 LEU cc_start: 0.7823 (mp) cc_final: 0.7607 (mp)
REVERT: C  107 ARG cc_start: 0.8169 (tpp80) cc_final: 0.7329 (tpt90)
  outliers start: 23
  outliers final: 14
  residues processed: 186
  average time/residue: 0.7627
  time to fit residues: 149.8008
Evaluate side-chains
  181 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 163
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  464 GLU
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  544 MET
Chi-restraints excluded: chain A residue  578 SER
Chi-restraints excluded: chain A residue  585 LYS
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  569 MET
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   93 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 112 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0470
   chunk 97 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 103 optimal weight:    0.0570
   chunk 96 optimal weight:    0.2980
   chunk 120 optimal weight:    1.9990
   chunk 119 optimal weight:    3.9990
   overall best weight:    0.3996

-------------------------------------------------------------------------------
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 = 0.3655 r_free = 0.3655 target = 0.140996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.108682 restraints weight = 19496.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.09
r_work: 0.3095 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2896
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2895 r_free = 0.2895    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2895
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.4129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10373  Z= 0.118
  Angle     :  0.569  11.749  14079  Z= 0.281
  Chirality :  0.038   0.138   1604
  Planarity :  0.004   0.056   1778
  Dihedral  :  5.997  83.232   1501
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.21 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.03 (0.24), residues: 1272
  helix:  2.06 (0.18), residues: 803
  sheet:  1.10 (0.45), residues: 124
  loop : -0.22 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 547 
 TYR   0.013   0.001   TYR A 541 
 PHE   0.027   0.001   PHE B  36 
 TRP   0.022   0.001   TRP C  36 
 HIS   0.003   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (10371)
  covalent geometry    : angle       0.56916 (14075)
  SS BOND              : bond        0.00076 (    2)
  SS BOND              : angle       0.11952 (    4)
  hydrogen bonds       : bond        0.04138 (  649)
  hydrogen bonds       : angle       3.69596 ( 1907)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 167
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A   72 LEU cc_start: 0.7701 (mm) cc_final: 0.7409 (OUTLIER)
REVERT: A   94 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8209 (tt0)
REVERT: A  127 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8262 (mmt90)
REVERT: A  199 ARG cc_start: 0.8259 (ttp-170) cc_final: 0.7278 (tpp80)
REVERT: A  277 TYR cc_start: 0.7748 (t80) cc_final: 0.7330 (t80)
REVERT: A  305 GLN cc_start: 0.8013 (mm110) cc_final: 0.7803 (mp10)
REVERT: A  354 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7949 (tp30)
REVERT: A  356 ARG cc_start: 0.8689 (mtp180) cc_final: 0.6899 (ptt90)
REVERT: A  371 GLU cc_start: 0.8117 (tp30) cc_final: 0.7726 (tp30)
REVERT: A  464 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7823 (mp0)
REVERT: A  525 THR cc_start: 0.8832 (p) cc_final: 0.8509 (p)
REVERT: A  534 LYS cc_start: 0.8444 (tttm) cc_final: 0.8209 (ttmt)
REVERT: A  560 ARG cc_start: 0.6368 (mmm160) cc_final: 0.5870 (mtm-85)
REVERT: A  585 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.6769 (ptmm)
REVERT: B   11 ARG cc_start: 0.8180 (ptp-170) cc_final: 0.7868 (ptp-110)
REVERT: B   35 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7083 (mp)
REVERT: B  164 TYR cc_start: 0.7824 (m-10) cc_final: 0.7564 (m-10)
REVERT: B  267 MET cc_start: 0.6777 (mmm) cc_final: 0.5957 (mmm)
REVERT: B  549 ARG cc_start: 0.8520 (pmm-80) cc_final: 0.8162 (ptm-80)
REVERT: C   65 LYS cc_start: 0.8747 (ttpp) cc_final: 0.8459 (ttpt)
REVERT: C  103 LEU cc_start: 0.7871 (mp) cc_final: 0.7661 (mp)
REVERT: C  107 ARG cc_start: 0.8198 (tpp80) cc_final: 0.7381 (tpt90)
  outliers start: 23
  outliers final: 13
  residues processed: 182
  average time/residue: 0.7257
  time to fit residues: 139.7586
Evaluate side-chains
  178 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 161
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  464 GLU
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  585 LYS
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  569 MET
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   93 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 123 optimal weight:    0.7980
   chunk 25 optimal weight:    0.1980
   chunk 62 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 40 optimal weight:    0.4980
   chunk 30 optimal weight:    0.7980
   chunk 99 optimal weight:    0.2980
   chunk 119 optimal weight:    0.2980
   chunk 71 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.3657 r_free = 0.3657 target = 0.141056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.106729 restraints weight = 14601.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 2.08
r_work: 0.3098 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2915
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2915
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.4166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10373  Z= 0.120
  Angle     :  0.579  11.559  14079  Z= 0.284
  Chirality :  0.038   0.138   1604
  Planarity :  0.004   0.055   1778
  Dihedral  :  5.931  81.099   1501
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 17.30 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.07 (0.24), residues: 1272
  helix:  2.07 (0.18), residues: 809
  sheet:  1.12 (0.45), residues: 124
  loop : -0.19 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 547 
 TYR   0.013   0.001   TYR A 125 
 PHE   0.030   0.001   PHE B  36 
 TRP   0.025   0.001   TRP C  36 
 HIS   0.003   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (10371)
  covalent geometry    : angle       0.57951 (14075)
  SS BOND              : bond        0.00105 (    2)
  SS BOND              : angle       0.10863 (    4)
  hydrogen bonds       : bond        0.04112 (  649)
  hydrogen bonds       : angle       3.67847 ( 1907)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 167
  time to evaluate  : 0.355 
Fit side-chains
REVERT: A   72 LEU cc_start: 0.7679 (mm) cc_final: 0.7390 (OUTLIER)
REVERT: A   94 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8173 (tt0)
REVERT: A  127 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8258 (mmt90)
REVERT: A  199 ARG cc_start: 0.8211 (ttp-170) cc_final: 0.7176 (tpp80)
REVERT: A  277 TYR cc_start: 0.7734 (t80) cc_final: 0.7364 (t80)
REVERT: A  305 GLN cc_start: 0.7966 (mm110) cc_final: 0.7765 (mp10)
REVERT: A  354 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7923 (tp30)
REVERT: A  356 ARG cc_start: 0.8683 (mtp180) cc_final: 0.6876 (ptt90)
REVERT: A  371 GLU cc_start: 0.8103 (tp30) cc_final: 0.7699 (tp30)
REVERT: A  464 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7796 (mp0)
REVERT: A  525 THR cc_start: 0.8820 (p) cc_final: 0.8526 (p)
REVERT: A  534 LYS cc_start: 0.8402 (tttm) cc_final: 0.8144 (ttmt)
REVERT: A  560 ARG cc_start: 0.6291 (mmm160) cc_final: 0.5892 (mtm-85)
REVERT: A  585 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.6798 (ptmm)
REVERT: B   11 ARG cc_start: 0.8201 (ptp-170) cc_final: 0.7850 (ptp-110)
REVERT: B   35 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7042 (mp)
REVERT: B  164 TYR cc_start: 0.7816 (m-10) cc_final: 0.7551 (m-10)
REVERT: B  248 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7182 (tt)
REVERT: B  267 MET cc_start: 0.6772 (mmm) cc_final: 0.5955 (mmm)
REVERT: B  549 ARG cc_start: 0.8501 (pmm-80) cc_final: 0.8128 (ptm-80)
REVERT: C   65 LYS cc_start: 0.8743 (ttpp) cc_final: 0.8464 (ttpt)
REVERT: C  103 LEU cc_start: 0.7837 (mp) cc_final: 0.7624 (mp)
REVERT: C  107 ARG cc_start: 0.8183 (tpp80) cc_final: 0.7359 (tpt90)
  outliers start: 21
  outliers final: 14
  residues processed: 180
  average time/residue: 0.7606
  time to fit residues: 144.6097
Evaluate side-chains
  184 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 165
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  464 GLU
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  585 LYS
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  569 MET
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   93 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 116 optimal weight:    0.0970
   chunk 123 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 75 optimal weight:    0.0470
   chunk 81 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 79 optimal weight:    0.4980
   overall best weight:    0.3876

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

Flipped N/Q/H residues before XYZ refinement:
C  57 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.141466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.107246 restraints weight = 14332.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 2.06
r_work: 0.3106 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2969
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2969 r_free = 0.2969    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2969 r_free = 0.2969    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2969
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.4222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10373  Z= 0.116
  Angle     :  0.565  11.437  14079  Z= 0.278
  Chirality :  0.038   0.138   1604
  Planarity :  0.004   0.055   1778
  Dihedral  :  5.850  78.753   1501
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 17.88 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.24), residues: 1272
  helix:  2.12 (0.18), residues: 806
  sheet:  1.15 (0.45), residues: 124
  loop : -0.17 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 547 
 TYR   0.013   0.001   TYR A 125 
 PHE   0.029   0.001   PHE B  36 
 TRP   0.027   0.001   TRP C  36 
 HIS   0.003   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (10371)
  covalent geometry    : angle       0.56516 (14075)
  SS BOND              : bond        0.00084 (    2)
  SS BOND              : angle       0.12931 (    4)
  hydrogen bonds       : bond        0.04030 (  649)
  hydrogen bonds       : angle       3.64925 ( 1907)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5050.06 seconds
wall clock time: 86 minutes 8.77 seconds (5168.77 seconds total)