Starting phenix.real_space_refine
on Fri Feb 14 13:13:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6rah_4775/02_2025/6rah_4775.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6rah_4775/02_2025/6rah_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6rah_4775/02_2025/6rah_4775.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6rah_4775/02_2025/6rah_4775.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6rah_4775/02_2025/6rah_4775.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6rah_4775/02_2025/6rah_4775.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 7.76, per 1000 atoms: 0.76
  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: 2.43
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  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: 1.00
  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: 3.23

  Time building geometry restraints manager: 2.86 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:             0.880
  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:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     27.620
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.050
  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:12.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.930
-------------------------------------------------------------------------------
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  10371  Z= 0.545
  Angle     :  1.529  18.793  14075  Z= 1.082
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.51 (0.20), 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
 TRP   0.055   0.003   TRP B 223 
 HIS   0.008   0.002   HIS A 554 
 PHE   0.038   0.003   PHE A 229 
 TYR   0.019   0.002   TYR A 299 
 ARG   0.026   0.001   ARG B  88 

*********************** 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  : 0.981 
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: 0.7712 (mt-10)
REVERT: A  477 GLU cc_start: 0.7534 (pt0) cc_final: 0.7194 (pt0)
REVERT: A  534 LYS cc_start: 0.8332 (tttm) cc_final: 0.8129 (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: 0.8142 (m)
REVERT: B   50 ASP cc_start: 0.7870 (m-30) cc_final: 0.7661 (m-30)
REVERT: B   63 LEU cc_start: 0.8028 (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: 0.7987 (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: 0.7091 (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: 1.7345
  time to fit residues: 461.3201
Evaluate side-chains
  179 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 107 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 99 optimal weight:    0.5980
   chunk 38 optimal weight:    0.4980
   chunk 60 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 115 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3678 r_free = 0.3678 target = 0.142826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.107127 restraints weight = 16673.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 2.25
r_work: 0.3080 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2905
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2905 r_free = 0.2905    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2905 r_free = 0.2905    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2905
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.2652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10371  Z= 0.239
  Angle     :  0.622   8.049  14075  Z= 0.322
  Chirality :  0.041   0.151   1604
  Planarity :  0.005   0.035   1778
  Dihedral  :  7.165  86.507   1501
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 12.24 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.22), residues: 1272
  helix:  0.48 (0.18), residues: 792
  sheet:  0.11 (0.43), residues: 129
  loop : -1.18 (0.30), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 223 
 HIS   0.005   0.001   HIS A  87 
 PHE   0.025   0.002   PHE B  36 
 TYR   0.014   0.001   TYR A 427 
 ARG   0.010   0.001   ARG B 512 

*********************** 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
  224 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 196
  time to evaluate  : 0.988 
Fit side-chains
REVERT: A   99 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8270 (mt0)
REVERT: A  183 VAL cc_start: 0.8453 (OUTLIER) cc_final: 0.8223 (p)
REVERT: A  255 ARG cc_start: 0.7714 (ttm110) cc_final: 0.7452 (ttp80)
REVERT: A  298 ASP cc_start: 0.7352 (t0) cc_final: 0.7018 (m-30)
REVERT: A  334 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7751 (tp30)
REVERT: A  354 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8183 (tt0)
REVERT: A  467 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7867 (tt0)
REVERT: A  477 GLU cc_start: 0.8193 (pt0) cc_final: 0.7743 (pt0)
REVERT: A  481 ARG cc_start: 0.8600 (mtt-85) cc_final: 0.8261 (mtt-85)
REVERT: A  534 LYS cc_start: 0.8499 (tttm) cc_final: 0.8253 (ttmt)
REVERT: B  164 TYR cc_start: 0.7648 (m-10) cc_final: 0.7424 (m-10)
REVERT: B  185 ARG cc_start: 0.8513 (ttt-90) cc_final: 0.8280 (mtp85)
REVERT: B  189 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8061 (mt-10)
REVERT: B  274 SER cc_start: 0.6821 (t) cc_final: 0.6396 (p)
REVERT: B  299 MET cc_start: 0.8442 (mtm) cc_final: 0.8011 (mtt)
REVERT: B  338 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7611 (mt-10)
REVERT: B  532 ARG cc_start: 0.8180 (mtm180) cc_final: 0.7972 (mtm180)
REVERT: B  549 ARG cc_start: 0.8481 (pmm-80) cc_final: 0.8132 (ptm-80)
REVERT: B  568 GLU cc_start: 0.8251 (tp30) cc_final: 0.8026 (tp30)
REVERT: C   80 HIS cc_start: 0.6464 (m-70) cc_final: 0.6232 (m-70)
REVERT: C   98 THR cc_start: 0.8134 (p) cc_final: 0.7798 (p)
REVERT: C  107 ARG cc_start: 0.8486 (tpp80) cc_final: 0.7539 (tpt90)
  outliers start: 28
  outliers final: 7
  residues processed: 209
  average time/residue: 1.5179
  time to fit residues: 336.6740
Evaluate side-chains
  184 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 172
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain C residue   99 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 92 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 71 optimal weight:    0.4980
   chunk 105 optimal weight:    0.6980
   chunk 79 optimal weight:    0.5980
   chunk 94 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 537 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.140349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.106746 restraints weight = 12432.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 1.86
r_work: 0.3114 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2917
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2917
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10371  Z= 0.215
  Angle     :  0.564   8.911  14075  Z= 0.290
  Chirality :  0.040   0.142   1604
  Planarity :  0.004   0.037   1778
  Dihedral  :  6.703  87.006   1501
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 13.96 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.23), residues: 1272
  helix:  1.31 (0.18), residues: 794
  sheet:  0.33 (0.43), residues: 129
  loop : -0.89 (0.31), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 223 
 HIS   0.005   0.001   HIS B 454 
 PHE   0.022   0.001   PHE B  36 
 TYR   0.012   0.001   TYR A 427 
 ARG   0.011   0.001   ARG B 512 

*********************** 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
  215 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 187
  time to evaluate  : 1.062 
Fit side-chains
REVERT: A   72 LEU cc_start: 0.7616 (mm) cc_final: 0.6900 (tt)
REVERT: A  127 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7385 (mpp-170)
REVERT: A  199 ARG cc_start: 0.8051 (ttp-170) cc_final: 0.7289 (tpp80)
REVERT: A  255 ARG cc_start: 0.7618 (ttm110) cc_final: 0.7394 (ttp80)
REVERT: A  354 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8018 (tt0)
REVERT: A  356 ARG cc_start: 0.8491 (mtp180) cc_final: 0.6834 (ptt90)
REVERT: A  467 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7727 (tt0)
REVERT: A  477 GLU cc_start: 0.8062 (pt0) cc_final: 0.7786 (pt0)
REVERT: A  534 LYS cc_start: 0.8625 (tttm) cc_final: 0.8370 (ttmt)
REVERT: B   35 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7743 (mp)
REVERT: B  164 TYR cc_start: 0.7714 (m-10) cc_final: 0.7468 (m-10)
REVERT: B  189 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8031 (mt-10)
REVERT: B  274 SER cc_start: 0.6734 (t) cc_final: 0.6337 (p)
REVERT: B  372 ARG cc_start: 0.8496 (mtp-110) cc_final: 0.8295 (mtp85)
REVERT: B  481 GLN cc_start: 0.9095 (mt0) cc_final: 0.8727 (mt0)
REVERT: B  532 ARG cc_start: 0.8331 (mtm180) cc_final: 0.7980 (mtm180)
REVERT: B  549 ARG cc_start: 0.8471 (pmm-80) cc_final: 0.8201 (ptm-80)
REVERT: B  568 GLU cc_start: 0.8196 (tp30) cc_final: 0.7974 (tp30)
REVERT: C   98 THR cc_start: 0.8160 (p) cc_final: 0.7794 (p)
REVERT: C  103 LEU cc_start: 0.7837 (mp) cc_final: 0.7629 (mp)
REVERT: C  107 ARG cc_start: 0.8292 (tpp80) cc_final: 0.7393 (tpt90)
  outliers start: 28
  outliers final: 12
  residues processed: 204
  average time/residue: 1.6346
  time to fit residues: 352.7473
Evaluate side-chains
  184 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 169
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
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  230 VAL
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  585 LYS
Chi-restraints excluded: chain B residue   32 LEU
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 C residue   93 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 102 optimal weight:    0.4980
   chunk 80 optimal weight:    0.5980
   chunk 120 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 82 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.7180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.140042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.103991 restraints weight = 19505.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 2.43
r_work: 0.3048 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2860
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2860 r_free = 0.2860    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2860 r_free = 0.2860    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2860
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.3475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10371  Z= 0.220
  Angle     :  0.569   9.639  14075  Z= 0.287
  Chirality :  0.040   0.139   1604
  Planarity :  0.004   0.045   1778
  Dihedral  :  6.614  88.312   1501
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 15.11 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.23), residues: 1272
  helix:  1.54 (0.18), residues: 803
  sheet:  0.60 (0.45), residues: 129
  loop : -0.83 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A  52 
 HIS   0.004   0.001   HIS A  87 
 PHE   0.024   0.001   PHE B  36 
 TYR   0.016   0.001   TYR A 541 
 ARG   0.011   0.000   ARG B 185 

*********************** 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
  209 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 179
  time to evaluate  : 1.210 
Fit side-chains
REVERT: A   52 TRP cc_start: 0.5752 (m-10) cc_final: 0.5442 (m-10)
REVERT: A   72 LEU cc_start: 0.7746 (mm) cc_final: 0.7398 (OUTLIER)
REVERT: A  127 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7334 (mpp-170)
REVERT: A  199 ARG cc_start: 0.8278 (ttp-170) cc_final: 0.7303 (tpp80)
REVERT: A  238 LYS cc_start: 0.8928 (mtpm) cc_final: 0.8538 (mttp)
REVERT: A  334 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7736 (tp30)
REVERT: A  356 ARG cc_start: 0.8707 (mtp180) cc_final: 0.6829 (ptt90)
REVERT: A  371 GLU cc_start: 0.8219 (tp30) cc_final: 0.7954 (tp30)
REVERT: A  467 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7795 (tt0)
REVERT: A  477 GLU cc_start: 0.8150 (pt0) cc_final: 0.7873 (pt0)
REVERT: A  481 ARG cc_start: 0.8536 (mtt-85) cc_final: 0.8232 (mtt-85)
REVERT: A  534 LYS cc_start: 0.8498 (tttm) cc_final: 0.8228 (ttmt)
REVERT: A  576 GLU cc_start: 0.7911 (tt0) cc_final: 0.7509 (tm-30)
REVERT: B   35 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7688 (mp)
REVERT: B  164 TYR cc_start: 0.7742 (m-10) cc_final: 0.7489 (m-10)
REVERT: B  267 MET cc_start: 0.6831 (mmm) cc_final: 0.6340 (mmm)
REVERT: B  274 SER cc_start: 0.6727 (t) cc_final: 0.6296 (p)
REVERT: B  481 GLN cc_start: 0.9105 (mt0) cc_final: 0.8751 (mt0)
REVERT: B  549 ARG cc_start: 0.8547 (pmm-80) cc_final: 0.8187 (ptm-80)
REVERT: C   83 MET cc_start: 0.6580 (mtm) cc_final: 0.6290 (mtm)
REVERT: C  107 ARG cc_start: 0.8256 (tpp80) cc_final: 0.7356 (tpt90)
  outliers start: 30
  outliers final: 15
  residues processed: 198
  average time/residue: 1.5258
  time to fit residues: 320.7260
Evaluate side-chains
  183 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
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  323 SER
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  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   93 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 94 optimal weight:    0.8980
   chunk 108 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 113 optimal weight:    0.0270
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.7038

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.139620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.105644 restraints weight = 21029.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 2.33
r_work: 0.3061 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2919
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2919 r_free = 0.2919    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2919 r_free = 0.2919    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2919
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.3682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10371  Z= 0.213
  Angle     :  0.552   9.124  14075  Z= 0.280
  Chirality :  0.040   0.138   1604
  Planarity :  0.004   0.049   1778
  Dihedral  :  6.517  89.352   1501
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 15.11 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.23), residues: 1272
  helix:  1.72 (0.18), residues: 806
  sheet:  0.70 (0.44), residues: 129
  loop : -0.74 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 223 
 HIS   0.004   0.001   HIS A  87 
 PHE   0.024   0.001   PHE B  36 
 TYR   0.014   0.001   TYR A 541 
 ARG   0.012   0.000   ARG B 185 

*********************** 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
  202 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 175
  time to evaluate  : 1.195 
Fit side-chains
REVERT: A   72 LEU cc_start: 0.7811 (mm) cc_final: 0.7439 (mt)
REVERT: A  127 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7350 (mpp-170)
REVERT: A  199 ARG cc_start: 0.8304 (ttp-170) cc_final: 0.7318 (tpp80)
REVERT: A  334 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7717 (tp30)
REVERT: A  356 ARG cc_start: 0.8657 (mtp180) cc_final: 0.6866 (ptt90)
REVERT: A  371 GLU cc_start: 0.8123 (tp30) cc_final: 0.7878 (tp30)
REVERT: A  464 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7760 (mp0)
REVERT: A  467 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7816 (tt0)
REVERT: A  477 GLU cc_start: 0.8148 (pt0) cc_final: 0.7873 (pt0)
REVERT: A  481 ARG cc_start: 0.8509 (mtt-85) cc_final: 0.8206 (mtt-85)
REVERT: A  525 THR cc_start: 0.8814 (p) cc_final: 0.8517 (p)
REVERT: A  534 LYS cc_start: 0.8440 (tttm) cc_final: 0.7986 (ttmt)
REVERT: A  576 GLU cc_start: 0.7878 (tt0) cc_final: 0.7518 (tm-30)
REVERT: B   35 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7494 (mp)
REVERT: B  164 TYR cc_start: 0.7789 (m-10) cc_final: 0.7537 (m-10)
REVERT: B  181 ARG cc_start: 0.8070 (ptp90) cc_final: 0.7763 (mtm-85)
REVERT: B  248 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7098 (tt)
REVERT: B  267 MET cc_start: 0.6899 (mmm) cc_final: 0.6366 (mmm)
REVERT: B  274 SER cc_start: 0.6713 (t) cc_final: 0.6368 (p)
REVERT: B  355 ARG cc_start: 0.9342 (OUTLIER) cc_final: 0.8768 (ttt-90)
REVERT: B  481 GLN cc_start: 0.9088 (mt0) cc_final: 0.8724 (mt0)
REVERT: B  549 ARG cc_start: 0.8501 (pmm-80) cc_final: 0.8188 (ptm-80)
REVERT: C   65 LYS cc_start: 0.8735 (ttpp) cc_final: 0.8422 (ttpt)
REVERT: C  103 LEU cc_start: 0.7889 (mp) cc_final: 0.7643 (mp)
REVERT: C  107 ARG cc_start: 0.8211 (tpp80) cc_final: 0.7344 (tpt90)
  outliers start: 27
  outliers final: 13
  residues processed: 193
  average time/residue: 1.6039
  time to fit residues: 327.5677
Evaluate side-chains
  188 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 169
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
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  323 SER
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  464 GLU
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  355 ARG
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 17 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 116 optimal weight:   20.0000
   chunk 40 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 126 optimal weight:    9.9990
   chunk 66 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B 191 GLN
C  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.137101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.102662 restraints weight = 14391.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 2.04
r_work: 0.3043 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2905
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2905 r_free = 0.2905    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2905 r_free = 0.2905    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2905
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.3838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10371  Z= 0.274
  Angle     :  0.589   9.326  14075  Z= 0.297
  Chirality :  0.041   0.138   1604
  Planarity :  0.004   0.054   1778
  Dihedral  :  6.910  85.814   1501
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 15.58 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.23), residues: 1272
  helix:  1.67 (0.18), residues: 807
  sheet:  0.78 (0.45), residues: 124
  loop : -0.64 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 223 
 HIS   0.005   0.001   HIS A  87 
 PHE   0.023   0.002   PHE B  36 
 TYR   0.014   0.001   TYR B 302 
 ARG   0.013   0.001   ARG A 560 

*********************** 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
  205 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 177
  time to evaluate  : 1.005 
Fit side-chains
REVERT: A  127 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7482 (mpp-170)
REVERT: A  199 ARG cc_start: 0.8401 (ttp-170) cc_final: 0.7347 (tpp80)
REVERT: A  238 LYS cc_start: 0.8874 (mtpm) cc_final: 0.8499 (mttp)
REVERT: A  334 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7766 (tp30)
REVERT: A  354 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8067 (tt0)
REVERT: A  356 ARG cc_start: 0.8656 (mtp180) cc_final: 0.6867 (ptt90)
REVERT: A  371 GLU cc_start: 0.8124 (tp30) cc_final: 0.7902 (tp30)
REVERT: A  467 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7803 (tt0)
REVERT: A  477 GLU cc_start: 0.8131 (pt0) cc_final: 0.7908 (pt0)
REVERT: A  525 THR cc_start: 0.8824 (p) cc_final: 0.8528 (p)
REVERT: B   35 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7473 (mp)
REVERT: B  164 TYR cc_start: 0.7826 (m-10) cc_final: 0.7566 (m-10)
REVERT: B  181 ARG cc_start: 0.8059 (ptp90) cc_final: 0.7766 (mtm-85)
REVERT: B  355 ARG cc_start: 0.9348 (OUTLIER) cc_final: 0.8639 (ttt-90)
REVERT: B  481 GLN cc_start: 0.9052 (mt0) cc_final: 0.8682 (mt0)
REVERT: B  532 ARG cc_start: 0.8228 (mtm180) cc_final: 0.7957 (mtm180)
REVERT: B  549 ARG cc_start: 0.8600 (pmm-80) cc_final: 0.8203 (ptm-80)
REVERT: C   65 LYS cc_start: 0.8738 (ttpp) cc_final: 0.8445 (ttpt)
REVERT: C   83 MET cc_start: 0.6751 (mtm) cc_final: 0.6333 (mtm)
REVERT: C  107 ARG cc_start: 0.8220 (tpp80) cc_final: 0.7376 (tpt90)
  outliers start: 28
  outliers final: 18
  residues processed: 194
  average time/residue: 1.6245
  time to fit residues: 333.2082
Evaluate side-chains
  191 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 168
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
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   94 GLU
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  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  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  301 LEU
Chi-restraints excluded: chain B residue  355 ARG
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 97 optimal weight:    0.6980
   chunk 30 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 303 GLN
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 = 0.137948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.103542 restraints weight = 14821.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 2.07
r_work: 0.3055 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2861
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2861 r_free = 0.2861    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2861 r_free = 0.2861    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2861
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.3963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10371  Z= 0.227
  Angle     :  0.572  12.702  14075  Z= 0.287
  Chirality :  0.040   0.154   1604
  Planarity :  0.004   0.051   1778
  Dihedral  :  6.631  85.504   1501
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 16.44 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.23), residues: 1272
  helix:  1.79 (0.18), residues: 806
  sheet:  0.84 (0.45), residues: 124
  loop : -0.60 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C  36 
 HIS   0.004   0.001   HIS A  87 
 PHE   0.024   0.001   PHE B  36 
 TYR   0.012   0.001   TYR A 541 
 ARG   0.014   0.000   ARG B 185 

*********************** 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
  200 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 171
  time to evaluate  : 1.128 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 LEU cc_start: 0.7939 (mm) cc_final: 0.7564 (mt)
REVERT: A  127 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7342 (mpp-170)
REVERT: A  199 ARG cc_start: 0.8333 (ttp-170) cc_final: 0.7325 (tpp80)
REVERT: A  238 LYS cc_start: 0.8878 (mtpm) cc_final: 0.8503 (mttp)
REVERT: A  354 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8048 (tt0)
REVERT: A  356 ARG cc_start: 0.8681 (mtp180) cc_final: 0.6917 (ptt90)
REVERT: A  371 GLU cc_start: 0.8192 (tp30) cc_final: 0.7976 (tp30)
REVERT: A  464 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7783 (mp0)
REVERT: A  467 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7868 (tt0)
REVERT: A  477 GLU cc_start: 0.8130 (pt0) cc_final: 0.7832 (pt0)
REVERT: A  481 ARG cc_start: 0.8458 (mtt-85) cc_final: 0.8162 (mtt-85)
REVERT: A  525 THR cc_start: 0.8835 (p) cc_final: 0.8508 (p)
REVERT: A  533 GLU cc_start: 0.8139 (tt0) cc_final: 0.7927 (tt0)
REVERT: A  537 GLN cc_start: 0.8215 (mt0) cc_final: 0.7992 (mt0)
REVERT: A  555 ARG cc_start: 0.7685 (mtm180) cc_final: 0.7478 (mtm180)
REVERT: A  569 ARG cc_start: 0.8667 (ttm170) cc_final: 0.8415 (ttm-80)
REVERT: B   35 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7405 (mp)
REVERT: B  164 TYR cc_start: 0.7828 (m-10) cc_final: 0.7608 (m-10)
REVERT: B  177 ARG cc_start: 0.7969 (mmm160) cc_final: 0.7662 (mmm-85)
REVERT: B  181 ARG cc_start: 0.8040 (ptp90) cc_final: 0.7750 (mtm-85)
REVERT: B  248 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7131 (tt)
REVERT: B  267 MET cc_start: 0.6932 (mmm) cc_final: 0.5831 (mmm)
REVERT: B  355 ARG cc_start: 0.9352 (OUTLIER) cc_final: 0.8605 (ttt-90)
REVERT: B  481 GLN cc_start: 0.9061 (mt0) cc_final: 0.8689 (mt0)
REVERT: B  549 ARG cc_start: 0.8565 (pmm-80) cc_final: 0.8211 (ptm-80)
REVERT: C   65 LYS cc_start: 0.8766 (ttpp) cc_final: 0.8482 (ttpt)
REVERT: C  107 ARG cc_start: 0.8239 (tpp80) cc_final: 0.7425 (tpt90)
  outliers start: 29
  outliers final: 14
  residues processed: 189
  average time/residue: 1.5790
  time to fit residues: 316.1081
Evaluate side-chains
  189 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 169
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
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  162 LEU
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  323 SER
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  260 VAL
Chi-restraints excluded: chain B residue  355 ARG
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 105 optimal weight:    0.9980
   chunk 104 optimal weight:    0.9990
   chunk 116 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 5 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.3608 r_free = 0.3608 target = 0.136856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.101656 restraints weight = 19654.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 2.39
r_work: 0.3011 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2870 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.4036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10371  Z= 0.257
  Angle     :  0.601  11.816  14075  Z= 0.297
  Chirality :  0.040   0.146   1604
  Planarity :  0.004   0.055   1778
  Dihedral  :  6.790  84.650   1501
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 16.63 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.23), residues: 1272
  helix:  1.75 (0.18), residues: 807
  sheet:  0.82 (0.44), residues: 124
  loop : -0.56 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 223 
 HIS   0.004   0.001   HIS A  87 
 PHE   0.024   0.002   PHE B  36 
 TYR   0.012   0.001   TYR B 302 
 ARG   0.014   0.001   ARG B 185 

*********************** 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
  204 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 175
  time to evaluate  : 1.136 
Fit side-chains
REVERT: A  127 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7442 (mpp-170)
REVERT: A  199 ARG cc_start: 0.8376 (ttp-170) cc_final: 0.7349 (tpp80)
REVERT: A  238 LYS cc_start: 0.8877 (mtpm) cc_final: 0.8512 (mttp)
REVERT: A  354 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8150 (tt0)
REVERT: A  356 ARG cc_start: 0.8668 (mtp180) cc_final: 0.6872 (ptt90)
REVERT: A  371 GLU cc_start: 0.8256 (tp30) cc_final: 0.8024 (tp30)
REVERT: A  464 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7821 (mp0)
REVERT: A  467 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7873 (tt0)
REVERT: A  477 GLU cc_start: 0.8171 (pt0) cc_final: 0.7882 (pt0)
REVERT: A  481 ARG cc_start: 0.8496 (mtt-85) cc_final: 0.8192 (mtt-85)
REVERT: A  525 THR cc_start: 0.8863 (p) cc_final: 0.8586 (p)
REVERT: A  538 GLU cc_start: 0.7951 (pt0) cc_final: 0.7718 (pt0)
REVERT: A  569 ARG cc_start: 0.8718 (ttm170) cc_final: 0.8483 (ttm-80)
REVERT: A  579 HIS cc_start: 0.7463 (OUTLIER) cc_final: 0.6946 (t70)
REVERT: B   35 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7354 (mp)
REVERT: B  164 TYR cc_start: 0.7880 (m-10) cc_final: 0.7654 (m-10)
REVERT: B  181 ARG cc_start: 0.8125 (ptp90) cc_final: 0.7840 (mtm-85)
REVERT: B  248 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7168 (tt)
REVERT: B  267 MET cc_start: 0.6804 (mmm) cc_final: 0.6009 (mmm)
REVERT: B  355 ARG cc_start: 0.9351 (OUTLIER) cc_final: 0.8630 (ttt-90)
REVERT: B  481 GLN cc_start: 0.9088 (mt0) cc_final: 0.8727 (mt0)
REVERT: B  549 ARG cc_start: 0.8593 (pmm-80) cc_final: 0.8185 (ptm-80)
REVERT: C   65 LYS cc_start: 0.8763 (ttpp) cc_final: 0.8476 (ttpt)
REVERT: C  107 ARG cc_start: 0.8255 (tpp80) cc_final: 0.7472 (tpt90)
  outliers start: 29
  outliers final: 17
  residues processed: 194
  average time/residue: 1.5564
  time to fit residues: 321.1609
Evaluate side-chains
  197 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 173
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
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   94 GLU
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  323 SER
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  579 HIS
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  355 ARG
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 8 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 25 optimal weight:    0.2980
   chunk 54 optimal weight:    1.9990
   chunk 78 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 125 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.6380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.138270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.105805 restraints weight = 20888.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 2.11
r_work: 0.3049 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2907
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2907 r_free = 0.2907    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2907 r_free = 0.2907    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2907
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.4123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10371  Z= 0.207
  Angle     :  0.573  11.653  14075  Z= 0.287
  Chirality :  0.039   0.143   1604
  Planarity :  0.004   0.058   1778
  Dihedral  :  6.487  86.328   1501
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.02 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.23), residues: 1272
  helix:  1.89 (0.18), residues: 803
  sheet:  0.90 (0.45), residues: 124
  loop : -0.46 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 223 
 HIS   0.004   0.001   HIS A  87 
 PHE   0.026   0.001   PHE B  36 
 TYR   0.011   0.001   TYR A 541 
 ARG   0.014   0.000   ARG A 547 

*********************** 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
  200 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 173
  time to evaluate  : 1.115 
Fit side-chains
REVERT: A   72 LEU cc_start: 0.7858 (mm) cc_final: 0.7491 (mt)
REVERT: A  127 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7357 (mpp-170)
REVERT: A  199 ARG cc_start: 0.8328 (ttp-170) cc_final: 0.7336 (tpp80)
REVERT: A  238 LYS cc_start: 0.8888 (mtpm) cc_final: 0.8529 (mttp)
REVERT: A  354 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8122 (tt0)
REVERT: A  356 ARG cc_start: 0.8672 (mtp180) cc_final: 0.6935 (ptt90)
REVERT: A  371 GLU cc_start: 0.8206 (tp30) cc_final: 0.7987 (tp30)
REVERT: A  464 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7815 (mp0)
REVERT: A  467 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7911 (tt0)
REVERT: A  477 GLU cc_start: 0.8145 (pt0) cc_final: 0.7859 (pt0)
REVERT: A  481 ARG cc_start: 0.8484 (mtt-85) cc_final: 0.8164 (mtt-85)
REVERT: A  525 THR cc_start: 0.8860 (p) cc_final: 0.8554 (p)
REVERT: A  560 ARG cc_start: 0.6405 (mmm160) cc_final: 0.5870 (mtm-85)
REVERT: B  132 MET cc_start: 0.8859 (ttp) cc_final: 0.8600 (ttp)
REVERT: B  164 TYR cc_start: 0.7849 (m-10) cc_final: 0.7619 (m-10)
REVERT: B  177 ARG cc_start: 0.7973 (mmm160) cc_final: 0.7616 (mmm-85)
REVERT: B  181 ARG cc_start: 0.8050 (ptp90) cc_final: 0.7762 (mtm-85)
REVERT: B  267 MET cc_start: 0.6804 (mmm) cc_final: 0.6059 (mmm)
REVERT: B  355 ARG cc_start: 0.9354 (OUTLIER) cc_final: 0.8616 (ttt-90)
REVERT: B  549 ARG cc_start: 0.8560 (pmm-80) cc_final: 0.8228 (ptm-80)
REVERT: C   65 LYS cc_start: 0.8770 (ttpp) cc_final: 0.8494 (ttpt)
REVERT: C  107 ARG cc_start: 0.8297 (tpp80) cc_final: 0.7547 (tpt90)
  outliers start: 27
  outliers final: 18
  residues processed: 190
  average time/residue: 1.5935
  time to fit residues: 320.9882
Evaluate side-chains
  192 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 170
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
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   94 GLU
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  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  585 LYS
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  355 ARG
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 85 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0970
   chunk 32 optimal weight:    0.9980
   chunk 100 optimal weight:    0.0970
   chunk 20 optimal weight:    0.5980
   chunk 7 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 97 optimal weight:    0.7980
   overall best weight:    0.4776

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.139191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.104990 restraints weight = 14377.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 2.04
r_work: 0.3076 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2927
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2927 r_free = 0.2927    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2927 r_free = 0.2927    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2927
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.4164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10371  Z= 0.186
  Angle     :  0.589  11.539  14075  Z= 0.290
  Chirality :  0.039   0.140   1604
  Planarity :  0.004   0.057   1778
  Dihedral  :  6.302  89.884   1501
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 17.59 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.23), residues: 1272
  helix:  1.97 (0.18), residues: 803
  sheet:  0.98 (0.45), residues: 124
  loop : -0.36 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 223 
 HIS   0.003   0.001   HIS A  87 
 PHE   0.028   0.001   PHE B  36 
 TYR   0.011   0.001   TYR B 302 
 ARG   0.019   0.001   ARG A 547 

********************** 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
  194 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 169
  time to evaluate  : 1.112 
Fit side-chains
REVERT: A   72 LEU cc_start: 0.7814 (mm) cc_final: 0.7480 (mt)
REVERT: A  127 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7325 (mpp-170)
REVERT: A  199 ARG cc_start: 0.8266 (ttp-170) cc_final: 0.7267 (tpp80)
REVERT: A  238 LYS cc_start: 0.8846 (mtpm) cc_final: 0.8481 (mttp)
REVERT: A  277 TYR cc_start: 0.7780 (t80) cc_final: 0.7365 (t80)
REVERT: A  354 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8067 (tt0)
REVERT: A  356 ARG cc_start: 0.8652 (mtp180) cc_final: 0.6911 (ptt90)
REVERT: A  371 GLU cc_start: 0.8188 (tp30) cc_final: 0.7751 (tp30)
REVERT: A  464 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7792 (mp0)
REVERT: A  467 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7847 (tt0)
REVERT: A  477 GLU cc_start: 0.8091 (pt0) cc_final: 0.7787 (pt0)
REVERT: A  525 THR cc_start: 0.8823 (p) cc_final: 0.8505 (p)
REVERT: A  533 GLU cc_start: 0.8205 (tt0) cc_final: 0.7950 (tt0)
REVERT: A  560 ARG cc_start: 0.6349 (mmm160) cc_final: 0.5876 (mtm-85)
REVERT: A  585 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.6924 (ptmm)
REVERT: B   35 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7081 (mp)
REVERT: B  164 TYR cc_start: 0.7825 (m-10) cc_final: 0.7574 (m-10)
REVERT: B  177 ARG cc_start: 0.7902 (mmm160) cc_final: 0.7591 (mmm-85)
REVERT: B  267 MET cc_start: 0.6668 (mmm) cc_final: 0.6039 (mmm)
REVERT: B  355 ARG cc_start: 0.9324 (OUTLIER) cc_final: 0.8603 (ttt-90)
REVERT: B  549 ARG cc_start: 0.8520 (pmm-80) cc_final: 0.8153 (ptm-80)
REVERT: C   65 LYS cc_start: 0.8780 (ttpp) cc_final: 0.8490 (ttpt)
REVERT: C  103 LEU cc_start: 0.7862 (mp) cc_final: 0.7660 (mp)
REVERT: C  107 ARG cc_start: 0.8216 (tpp80) cc_final: 0.7449 (tpt90)
  outliers start: 25
  outliers final: 17
  residues processed: 185
  average time/residue: 1.5494
  time to fit residues: 303.5411
Evaluate side-chains
  187 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 164
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
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   94 GLU
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  370 THR
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  355 ARG
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 59 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 107 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 116 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 126 optimal weight:    1.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.3612 r_free = 0.3612 target = 0.137165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.103239 restraints weight = 14348.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 2.02
r_work: 0.3052 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2866
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    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 = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.4198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10371  Z= 0.252
  Angle     :  0.614  11.330  14075  Z= 0.305
  Chirality :  0.040   0.145   1604
  Planarity :  0.004   0.055   1778
  Dihedral  :  6.658  88.467   1501
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 17.78 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.23), residues: 1272
  helix:  1.86 (0.18), residues: 802
  sheet:  0.95 (0.44), residues: 124
  loop : -0.43 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 223 
 HIS   0.004   0.001   HIS A  87 
 PHE   0.028   0.002   PHE B  36 
 TYR   0.012   0.001   TYR B 110 
 ARG   0.018   0.001   ARG A 547 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10037.19 seconds
wall clock time: 176 minutes 50.22 seconds (10610.22 seconds total)