Starting phenix.real_space_refine
on Wed Sep 17 23:41:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y04_33537/09_2025/7y04_33537.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y04_33537/09_2025/7y04_33537.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y04_33537/09_2025/7y04_33537.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y04_33537/09_2025/7y04_33537.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y04_33537/09_2025/7y04_33537.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y04_33537/09_2025/7y04_33537.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.104
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: 7
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      58      5.16       5
     Be      2      3.05       5
     C    7612      2.51       5
     N    2041      2.21       5
     O    2327      1.98       5
     F       6      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12050
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 5038
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 623, 5038
          Classifications: {'peptide': 623}
          Link IDs: {'PTRANS': 17, 'TRANS': 605}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5021
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 621, 5021
          Classifications: {'peptide': 621}
          Link IDs: {'PTRANS': 17, 'TRANS': 603}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 928
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 3, 'TRANS': 107}
    Chain: "D"
      Number of atoms: 928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 928
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 3, 'TRANS': 107}
    Chain: "E"
      Number of atoms: 73
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 73
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 31
          Unusual residues: {'ADP': 1, 'BEF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 31
          Unusual residues: {'ADP': 1, 'BEF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.09, per 1000 atoms: 0.26
  Number of scatterers: 12050
  At special positions: 0
  Unit cell: (107, 93.09, 136.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      58     16.00
     P       4     15.00
     F       6      9.00
     O    2327      8.00
     N    2041      7.00
     C    7612      6.00
     Be      2      4.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.99
  Conformation dependent library (CDL) restraints added in 549.9 milliseconds
  
  Enol-peptide restraints added in 13.6 microseconds
  

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2818

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 15 sheets defined
      37.3% alpha, 15.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 31
      removed outlier: 4.072A  pdb=" N   SER A  26 " --> pdb=" O   ALA A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 58
    Processing helix  chain 'A' and resid 63 through 68
      removed outlier: 4.231A  pdb=" N   SER A  67 " --> pdb=" O   LYS A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 102
    Processing helix  chain 'A' and resid 108 through 116
      removed outlier: 3.828A  pdb=" N   ALA A 112 " --> pdb=" O   SER A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 138
      removed outlier: 3.797A  pdb=" N   TYR A 137 " --> pdb=" O   TYR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 193
      removed outlier: 3.727A  pdb=" N   TYR A 192 " --> pdb=" O   GLN A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 207
      removed outlier: 3.627A  pdb=" N   VAL A 198 " --> pdb=" O   GLU A 194 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   GLN A 207 " --> pdb=" O   LYS A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 296
    Processing helix  chain 'A' and resid 299 through 310
    Processing helix  chain 'A' and resid 366 through 370
    Processing helix  chain 'A' and resid 371 through 375
    Processing helix  chain 'A' and resid 400 through 421
      removed outlier: 3.744A  pdb=" N   ILE A 404 " --> pdb=" O   ILE A 400 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LYS A 406 " --> pdb=" O   LYS A 402 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   LYS A 410 " --> pdb=" O   LYS A 406 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LYS A 411 " --> pdb=" O   ASN A 407 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLU A 414 " --> pdb=" O   LYS A 410 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   GLU A 421 " --> pdb=" O   SER A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 444
      removed outlier: 3.811A  pdb=" N   ALA A 432 " --> pdb=" O   LYS A 428 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   LYS A 435 " --> pdb=" O   GLU A 431 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   ASN A 436 " --> pdb=" O   ALA A 432 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU A 437 " --> pdb=" O   PHE A 433 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   HIS A 442 " --> pdb=" O   LYS A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 476
    Processing helix  chain 'A' and resid 490 through 496
      removed outlier: 3.642A  pdb=" N   VAL A 494 " --> pdb=" O   SER A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 501
    Processing helix  chain 'A' and resid 502 through 507
    Processing helix  chain 'A' and resid 516 through 525
      removed outlier: 4.353A  pdb=" N   TYR A 520 " --> pdb=" O   PRO A 516 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   GLN A 524 " --> pdb=" O   TYR A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 560
      removed outlier: 3.596A  pdb=" N   LYS A 550 " --> pdb=" O   ASP A 546 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LYS A 551 " --> pdb=" O   GLU A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 571
    Processing helix  chain 'A' and resid 599 through 607
      removed outlier: 3.724A  pdb=" N   GLU A 603 " --> pdb=" O   THR A 599 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   ARG A 604 " --> pdb=" O   ALA A 600 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE A 605 " --> pdb=" O   ASN A 601 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 645
      removed outlier: 3.548A  pdb=" N   LEU A 638 " --> pdb=" O   ILE A 634 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLN A 640 " --> pdb=" O   GLU A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 664
      removed outlier: 4.098A  pdb=" N   VAL A 656 " --> pdb=" O   LYS A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 689
      removed outlier: 3.557A  pdb=" N   ARG A 679 " --> pdb=" O   THR A 675 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 31
    Processing helix  chain 'B' and resid 38 through 58
    Processing helix  chain 'B' and resid 61 through 68
      removed outlier: 3.866A  pdb=" N   LEU B  65 " --> pdb=" O   PRO B  62 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   SER B  67 " --> pdb=" O   LYS B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 102
    Processing helix  chain 'B' and resid 108 through 115
      removed outlier: 3.723A  pdb=" N   ALA B 112 " --> pdb=" O   SER B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 139
      removed outlier: 3.743A  pdb=" N   TYR B 137 " --> pdb=" O   TYR B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 193
      removed outlier: 3.640A  pdb=" N   TYR B 192 " --> pdb=" O   GLN B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 206
    Processing helix  chain 'B' and resid 292 through 296
      removed outlier: 3.537A  pdb=" N   ILE B 296 " --> pdb=" O   PRO B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 310
      removed outlier: 3.544A  pdb=" N   SER B 307 " --> pdb=" O   GLU B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 375
    Processing helix  chain 'B' and resid 399 through 401
      No H-bonds generated for 'chain 'B' and resid 399 through 401'
    Processing helix  chain 'B' and resid 402 through 421
      removed outlier: 3.868A  pdb=" N   LYS B 406 " --> pdb=" O   LYS B 402 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLU B 414 " --> pdb=" O   LYS B 410 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   SER B 417 " --> pdb=" O   LEU B 413 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLU B 421 " --> pdb=" O   SER B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 431
      removed outlier: 3.781A  pdb=" N   LYS B 427 " --> pdb=" O   LYS B 423 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   LYS B 428 " --> pdb=" O   GLU B 424 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   PHE B 429 " --> pdb=" O   ASN B 425 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 444
      removed outlier: 4.189A  pdb=" N   LEU B 437 " --> pdb=" O   PHE B 433 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   HIS B 442 " --> pdb=" O   LYS B 438 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 452
    Processing helix  chain 'B' and resid 469 through 475
      removed outlier: 3.583A  pdb=" N   SER B 474 " --> pdb=" O   SER B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 490 through 497
      removed outlier: 3.699A  pdb=" N   ASN B 496 " --> pdb=" O   GLU B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 499 through 504
      removed outlier: 4.702A  pdb=" N   VAL B 503 " --> pdb=" O   PHE B 499 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 516 through 526
      removed outlier: 4.165A  pdb=" N   TYR B 520 " --> pdb=" O   PRO B 516 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLN B 524 " --> pdb=" O   TYR B 520 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LYS B 526 " --> pdb=" O   VAL B 522 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 546 through 560
    Processing helix  chain 'B' and resid 561 through 572
    Processing helix  chain 'B' and resid 599 through 606
      removed outlier: 3.745A  pdb=" N   ARG B 604 " --> pdb=" O   ALA B 600 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 615 through 619
    Processing helix  chain 'B' and resid 632 through 645
      removed outlier: 3.757A  pdb=" N   GLN B 640 " --> pdb=" O   GLU B 636 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LYS B 641 " --> pdb=" O   THR B 637 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 666
      removed outlier: 4.133A  pdb=" N   VAL B 656 " --> pdb=" O   LYS B 652 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 672 through 689
      removed outlier: 4.324A  pdb=" N   HIS B 676 " --> pdb=" O   ASP B 672 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   LYS B 685 " --> pdb=" O   TYR B 681 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU B 686 " --> pdb=" O   ARG B 682 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   GLY B 687 " --> pdb=" O   MET B 683 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 15
      removed outlier: 3.861A  pdb=" N   GLU A  13 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   PHE B 165 " --> pdb=" O   PHE A  15 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LEU B 183 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LEU B  84 " --> pdb=" O   LEU B 183 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   THR B  83 " --> pdb=" O   ASN B  78 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ASN B  78 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   THR B  85 " --> pdb=" O   ILE B  76 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ILE B  76 " --> pdb=" O   THR B  85 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   THR B 214 " --> pdb=" O   ILE B  73 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   LEU B 215 " --> pdb=" O   GLU B 280 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   GLU B 280 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 281
      removed outlier: 4.036A  pdb=" N   GLU A 280 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   LEU A 215 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR A 214 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   VAL A  87 " --> pdb=" O   ASP A  74 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   VAL A 181 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLU A 158 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   PHE A 165 " --> pdb=" O   PHE B  15 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   PHE B  15 " --> pdb=" O   PHE A 165 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 105
    Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 323
      removed outlier: 3.844A  pdb=" N   ALA A 317 " --> pdb=" O   ILE A 335 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   PHE A 321 " --> pdb=" O   ALA A 331 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   PHE A 329 " --> pdb=" O   VAL A 323 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LYS A 354 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   MET A 363 " --> pdb=" O   LEU A 355 " (cutoff:3.500A)
      removed outlier: 6.011A  pdb=" N   VAL A 357 " --> pdb=" O   PHE A 361 " (cutoff:3.500A)
      removed outlier: 5.633A  pdb=" N   PHE A 361 " --> pdb=" O   VAL A 357 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 456 through 457
    Processing sheet with id=AA6, first strand: chain 'A' and resid 511 through 513
      removed outlier: 5.586A  pdb=" N   ILE A 483 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 591 through 592
    Processing sheet with id=AA8, first strand: chain 'B' and resid 317 through 323
      removed outlier: 3.844A  pdb=" N   ALA B 317 " --> pdb=" O   ILE B 335 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   PHE B 321 " --> pdb=" O   ALA B 331 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   PHE B 329 " --> pdb=" O   VAL B 323 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LYS B 354 " --> pdb=" O   GLY B 379 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   ILE B 353 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
      removed outlier: 5.424A  pdb=" N   ASP B 364 " --> pdb=" O   ILE B 353 " (cutoff:3.500A)
      removed outlier: 7.311A  pdb=" N   LEU B 355 " --> pdb=" O   ILE B 362 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 456 through 457
    Processing sheet with id=AB1, first strand: chain 'B' and resid 511 through 513
      removed outlier: 5.664A  pdb=" N   ILE B 483 " --> pdb=" O   VAL B 534 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 591 through 592
    Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 68
      removed outlier: 7.179A  pdb=" N   ASP C  63 " --> pdb=" O   ARG C  78 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   ARG C  78 " --> pdb=" O   ASP C  63 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LEU C  74 " --> pdb=" O   LYS C  67 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   ALA C   6 " --> pdb=" O   SER C 100 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 24 through 30
      removed outlier: 4.853A  pdb=" N   ASP C  26 " --> pdb=" O   LEU C  41 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   LEU C  41 " --> pdb=" O   ASP C  26 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 59 through 68
      removed outlier: 7.160A  pdb=" N   ASP D  63 " --> pdb=" O   ARG D  78 " (cutoff:3.500A)
      removed outlier: 5.335A  pdb=" N   ARG D  78 " --> pdb=" O   ASP D  63 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU D  74 " --> pdb=" O   LYS D  67 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ALA D   6 " --> pdb=" O   SER D 100 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 24 through 31
      removed outlier: 5.091A  pdb=" N   ASP D  26 " --> pdb=" O   LEU D  41 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   LEU D  41 " --> pdb=" O   ASP D  26 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   HIS D  49 " --> pdb=" O   CYS D  40 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   PHE D  47 " --> pdb=" O   GLY D  42 " (cutoff:3.500A)

    427 hydrogen bonds defined for protein.
    1152 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.93

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 2075
        1.30 -     1.43: 3001
        1.43 -     1.56: 7086
        1.56 -     1.69: 10
        1.69 -     1.81: 94
  Bond restraints: 12266
  Sorted by residual:
  bond pdb=" CA  THR E 276 "
       pdb=" C   THR E 276 "
    ideal  model  delta    sigma   weight residual
    1.533  1.473  0.060 5.60e-03 3.19e+04 1.15e+02
  bond pdb=" CA  GLU A  13 "
       pdb=" CB  GLU A  13 "
    ideal  model  delta    sigma   weight residual
    1.530  1.448  0.082 1.48e-02 4.57e+03 3.08e+01
  bond pdb=" C4  ADP B 801 "
       pdb=" C5  ADP B 801 "
    ideal  model  delta    sigma   weight residual
    1.490  1.385  0.105 2.00e-02 2.50e+03 2.77e+01
  bond pdb=" C4  ADP A 801 "
       pdb=" C5  ADP A 801 "
    ideal  model  delta    sigma   weight residual
    1.490  1.385  0.105 2.00e-02 2.50e+03 2.77e+01
  bond pdb=" N   THR E 276 "
       pdb=" CA  THR E 276 "
    ideal  model  delta    sigma   weight residual
    1.457  1.425  0.032 6.40e-03 2.44e+04 2.48e+01
  ... (remaining 12261 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.27: 16387
        3.27 -     6.54: 92
        6.54 -     9.81: 18
        9.81 -    13.08: 6
       13.08 -    16.34: 2
  Bond angle restraints: 16505
  Sorted by residual:
  angle pdb=" C   THR E 276 "
        pdb=" CA  THR E 276 "
        pdb=" CB  THR E 276 "
      ideal   model   delta    sigma   weight residual
     117.07  105.50   11.57 1.44e+00 4.82e-01 6.46e+01
  angle pdb=" CA  THR E 276 "
        pdb=" C   THR E 276 "
        pdb=" N   LYS E 277 "
      ideal   model   delta    sigma   weight residual
     120.47  114.61    5.86 1.03e+00 9.43e-01 3.24e+01
  angle pdb=" CA  GLU A  13 "
        pdb=" C   GLU A  13 "
        pdb=" N   THR A  14 "
      ideal   model   delta    sigma   weight residual
     115.86  122.91   -7.05 1.24e+00 6.50e-01 3.23e+01
  angle pdb=" PA  ADP B 801 "
        pdb=" O3A ADP B 801 "
        pdb=" PB  ADP B 801 "
      ideal   model   delta    sigma   weight residual
     120.50  136.84  -16.34 3.00e+00 1.11e-01 2.97e+01
  angle pdb=" PA  ADP A 801 "
        pdb=" O3A ADP A 801 "
        pdb=" PB  ADP A 801 "
      ideal   model   delta    sigma   weight residual
     120.50  136.80  -16.30 3.00e+00 1.11e-01 2.95e+01
  ... (remaining 16500 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.40: 7251
       30.40 -    60.81: 244
       60.81 -    91.21: 27
       91.21 -   121.62: 1
      121.62 -   152.02: 3
  Dihedral angle restraints: 7526
    sinusoidal: 3190
      harmonic: 4336
  Sorted by residual:
  dihedral pdb=" O2A ADP A 801 "
           pdb=" O3A ADP A 801 "
           pdb=" PA  ADP A 801 "
           pdb=" PB  ADP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  147.98  152.02     1      2.00e+01 2.50e-03 4.52e+01
  dihedral pdb=" O2A ADP B 801 "
           pdb=" O3A ADP B 801 "
           pdb=" PA  ADP B 801 "
           pdb=" PB  ADP B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  149.00  151.01     1      2.00e+01 2.50e-03 4.50e+01
  dihedral pdb=" C5' ADP A 801 "
           pdb=" O5' ADP A 801 "
           pdb=" PA  ADP A 801 "
           pdb=" O2A ADP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  173.79  126.21     1      2.00e+01 2.50e-03 3.82e+01
  ... (remaining 7523 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1396
       0.047 -    0.095: 312
       0.095 -    0.142: 92
       0.142 -    0.189: 11
       0.189 -    0.236: 1
  Chirality restraints: 1812
  Sorted by residual:
  chirality pdb=" CA  GLU E 273 "
            pdb=" N   GLU E 273 "
            pdb=" C   GLU E 273 "
            pdb=" CB  GLU E 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CA  ARG A 392 "
            pdb=" N   ARG A 392 "
            pdb=" C   ARG A 392 "
            pdb=" CB  ARG A 392 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.06e-01
  chirality pdb=" CA  GLU B 418 "
            pdb=" N   GLU B 418 "
            pdb=" C   GLU B 418 "
            pdb=" CB  GLU B 418 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.25e-01
  ... (remaining 1809 not shown)

  Planarity restraints: 2105
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E 272 "    0.012 2.00e-02 2.50e+03   2.40e-02 5.76e+00
        pdb=" C   LEU E 272 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   LEU E 272 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLU E 273 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE E 274 "   -0.011 2.00e-02 2.50e+03   2.16e-02 4.66e+00
        pdb=" C   ILE E 274 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ILE E 274 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ARG E 275 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR E 276 "   -0.010 2.00e-02 2.50e+03   1.99e-02 3.95e+00
        pdb=" C   THR E 276 "    0.034 2.00e-02 2.50e+03
        pdb=" O   THR E 276 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LYS E 277 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 2102 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1398
        2.75 -     3.29: 11492
        3.29 -     3.83: 17824
        3.83 -     4.36: 21066
        4.36 -     4.90: 37507
  Nonbonded interactions: 89287
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  56 "
            pdb=" OE1 GLN B 118 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" OE1 GLU A 548 "
            pdb=" NZ  LYS A 551 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" O   ILE B 353 "
            pdb=" OG  SER B 365 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OH  TYR A 457 "
            pdb=" OD1 ASP A 518 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" NZ  LYS A 199 "
            pdb=" OE2 GLU A 280 "
     model   vdw
     2.275 3.120
  ... (remaining 89282 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 10 through 217 or resid 278 through 802))
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.110
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6347
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      :  0.010   0.693  12268  Z= 0.907
  Angle     :  0.763  16.344  16505  Z= 0.397
  Chirality :  0.044   0.236   1812
  Planarity :  0.004   0.049   2105
  Dihedral  : 15.694 152.020   4708
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  0.37 %
    Favored  : 98.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.60 (0.21), residues: 1461
  helix: -0.78 (0.23), residues: 489
  sheet: -2.78 (0.27), residues: 294
  loop : -1.83 (0.22), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 338 
 TYR   0.012   0.001   TYR A 681 
 PHE   0.013   0.001   PHE C  38 
 TRP   0.024   0.002   TRP B 157 
 HIS   0.006   0.001   HIS D  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 (12266)
  covalent geometry    : angle       0.76275 (16505)
  hydrogen bonds       : bond        0.22018 (  427)
  hydrogen bonds       : angle       8.09700 ( 1152)
  Misc. bond           : bond        0.68185 (    2)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 197
  time to evaluate  : 0.440 
Fit side-chains
REVERT: A  280 GLU cc_start: 0.7466 (tt0) cc_final: 0.7220 (pt0)
REVERT: A  372 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7686 (tm-30)
REVERT: A  546 ASP cc_start: 0.7582 (t70) cc_final: 0.7018 (t70)
REVERT: A  550 LYS cc_start: 0.7535 (mptt) cc_final: 0.7215 (mmtt)
REVERT: A  577 LYS cc_start: 0.7619 (ptmm) cc_final: 0.7231 (ptpp)
REVERT: A  629 ASN cc_start: 0.8596 (t0) cc_final: 0.8238 (t0)
REVERT: B   11 GLU cc_start: 0.5731 (OUTLIER) cc_final: 0.5139 (pm20)
REVERT: B  552 LYS cc_start: 0.8410 (tmtt) cc_final: 0.8185 (tptt)
REVERT: B  553 MET cc_start: 0.9073 (tmm) cc_final: 0.8715 (tmm)
REVERT: B  573 LYS cc_start: 0.8711 (tppt) cc_final: 0.8152 (ttpp)
REVERT: B  629 ASN cc_start: 0.8856 (t0) cc_final: 0.8620 (t0)
REVERT: C   47 PHE cc_start: 0.6818 (m-80) cc_final: 0.6386 (m-10)
REVERT: C  104 ASN cc_start: 0.8057 (m-40) cc_final: 0.7844 (m-40)
REVERT: D   37 THR cc_start: 0.7093 (t) cc_final: 0.6751 (p)
REVERT: D   81 GLU cc_start: 0.7428 (mp0) cc_final: 0.6999 (mp0)
REVERT: E  273 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7308 (tm-30)
REVERT: E  275 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.6710 (tmt170)
  outliers start: 10
  outliers final: 1
  residues processed: 203
  average time/residue: 0.1382
  time to fit residues: 38.3147
Evaluate side-chains
  162 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 158
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 GLU
Chi-restraints excluded: chain E residue  270 SER
Chi-restraints excluded: chain E residue  273 GLU
Chi-restraints excluded: chain E residue  275 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 640 GLN
B 100 ASN
C  57 HIS
C  84 GLN
D  57 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.146763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.110585 restraints weight = 15092.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.117334 restraints weight = 8704.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.120564 restraints weight = 4748.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.121551 restraints weight = 3510.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.121925 restraints weight = 3265.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.1261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12268  Z= 0.199
  Angle     :  0.662   7.598  16505  Z= 0.338
  Chirality :  0.045   0.175   1812
  Planarity :  0.004   0.045   2105
  Dihedral  :  8.920 151.774   1626
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  7.92 %
    Favored  : 90.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.23 (0.21), residues: 1461
  helix: -0.38 (0.24), residues: 496
  sheet: -2.33 (0.29), residues: 285
  loop : -1.86 (0.22), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 378 
 TYR   0.013   0.002   TYR A 305 
 PHE   0.014   0.002   PHE D  38 
 TRP   0.027   0.002   TRP B 157 
 HIS   0.006   0.001   HIS B 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (12266)
  covalent geometry    : angle       0.66187 (16505)
  hydrogen bonds       : bond        0.05093 (  427)
  hydrogen bonds       : angle       5.75170 ( 1152)
  Misc. bond           : bond        0.00227 (    2)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 161
  time to evaluate  : 0.507 
Fit side-chains
REVERT: A   11 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6276 (pm20)
REVERT: A  501 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7844 (mt-10)
REVERT: A  546 ASP cc_start: 0.8025 (t70) cc_final: 0.7238 (t70)
REVERT: A  550 LYS cc_start: 0.8053 (mptt) cc_final: 0.7537 (mmtt)
REVERT: A  577 LYS cc_start: 0.8213 (ptmm) cc_final: 0.7733 (ptpp)
REVERT: A  623 LYS cc_start: 0.7129 (mttt) cc_final: 0.6926 (mtpt)
REVERT: A  629 ASN cc_start: 0.8901 (t0) cc_final: 0.8542 (t0)
REVERT: A  652 LYS cc_start: 0.8196 (mttp) cc_final: 0.7994 (mttp)
REVERT: B  100 ASN cc_start: 0.7398 (OUTLIER) cc_final: 0.7087 (t0)
REVERT: B  424 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8099 (tm-30)
REVERT: B  471 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6664 (mt-10)
REVERT: B  553 MET cc_start: 0.9184 (tmm) cc_final: 0.8744 (tmm)
REVERT: B  573 LYS cc_start: 0.8622 (tppt) cc_final: 0.8152 (ttpp)
REVERT: B  629 ASN cc_start: 0.9071 (t0) cc_final: 0.8840 (t0)
REVERT: C    9 TYR cc_start: 0.6853 (p90) cc_final: 0.6436 (p90)
REVERT: C   47 PHE cc_start: 0.7438 (m-80) cc_final: 0.7024 (m-10)
REVERT: D   81 GLU cc_start: 0.7906 (mp0) cc_final: 0.7371 (mp0)
  outliers start: 20
  outliers final: 11
  residues processed: 174
  average time/residue: 0.1232
  time to fit residues: 29.9982
Evaluate side-chains
  159 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 146
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 GLU
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  464 ASP
Chi-restraints excluded: chain A residue  487 THR
Chi-restraints excluded: chain B residue  100 ASN
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  476 MET
Chi-restraints excluded: chain C residue   58 CYS
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain E residue  273 GLU
Chi-restraints excluded: chain E residue  275 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 54 optimal weight:    7.9990
   chunk 28 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 32 optimal weight:    0.5980
   chunk 105 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 125 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
B 100 ASN
D  57 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.160848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.130126 restraints weight = 14282.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.134052 restraints weight = 10608.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.135963 restraints weight = 7241.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.136263 restraints weight = 5967.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.136899 restraints weight = 5511.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  12268  Z= 0.134
  Angle     :  0.582   7.585  16505  Z= 0.297
  Chirality :  0.043   0.159   1812
  Planarity :  0.003   0.040   2105
  Dihedral  :  7.993 142.859   1622
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 10.60 %
    Favored  : 87.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.90 (0.22), residues: 1461
  helix: -0.10 (0.25), residues: 492
  sheet: -1.92 (0.29), residues: 298
  loop : -1.76 (0.22), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 378 
 TYR   0.011   0.001   TYR A 305 
 PHE   0.011   0.001   PHE D  38 
 TRP   0.023   0.001   TRP B 157 
 HIS   0.004   0.001   HIS B 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (12266)
  covalent geometry    : angle       0.58209 (16505)
  hydrogen bonds       : bond        0.04118 (  427)
  hydrogen bonds       : angle       5.28664 ( 1152)
  Misc. bond           : bond        0.00146 (    2)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 157
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
REVERT: A  398 SER cc_start: 0.9069 (m) cc_final: 0.8772 (t)
REVERT: A  546 ASP cc_start: 0.7888 (t70) cc_final: 0.7309 (t70)
REVERT: A  550 LYS cc_start: 0.8195 (mptt) cc_final: 0.7748 (mmtt)
REVERT: A  652 LYS cc_start: 0.8319 (mttp) cc_final: 0.8087 (mttp)
REVERT: B  100 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7543 (t0)
REVERT: B  553 MET cc_start: 0.8793 (tmm) cc_final: 0.8540 (tmm)
REVERT: B  617 MET cc_start: 0.8443 (mpp) cc_final: 0.8069 (mpp)
REVERT: D   81 GLU cc_start: 0.7967 (mp0) cc_final: 0.7603 (mp0)
REVERT: E  273 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7840 (tm-30)
REVERT: E  275 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7060 (tmt170)
  outliers start: 19
  outliers final: 10
  residues processed: 168
  average time/residue: 0.1231
  time to fit residues: 28.9988
Evaluate side-chains
  153 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 140
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  309 THR
Chi-restraints excluded: chain A residue  487 THR
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain B residue  100 ASN
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  476 MET
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain C residue   58 CYS
Chi-restraints excluded: chain E residue  273 GLU
Chi-restraints excluded: chain E residue  275 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 104 optimal weight:    6.9990
   chunk 139 optimal weight:    9.9990
   chunk 75 optimal weight:    0.9990
   chunk 89 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0980
   chunk 7 optimal weight:    0.9980
   chunk 122 optimal weight:    5.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 523 GLN
B 100 ASN
C  84 GLN
D  57 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.156846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.125557 restraints weight = 14335.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.130309 restraints weight = 9738.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.131245 restraints weight = 6612.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.133892 restraints weight = 5172.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.134066 restraints weight = 4401.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  12268  Z= 0.147
  Angle     :  0.580   7.612  16505  Z= 0.295
  Chirality :  0.043   0.153   1812
  Planarity :  0.003   0.040   2105
  Dihedral  :  7.896 173.499   1622
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 11.95 %
    Favored  : 86.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.78 (0.22), residues: 1461
  helix:  0.02 (0.25), residues: 494
  sheet: -1.74 (0.29), residues: 298
  loop : -1.78 (0.22), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 338 
 TYR   0.015   0.001   TYR C   9 
 PHE   0.013   0.001   PHE A  32 
 TRP   0.023   0.001   TRP B 157 
 HIS   0.004   0.001   HIS B 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (12266)
  covalent geometry    : angle       0.58001 (16505)
  hydrogen bonds       : bond        0.03933 (  427)
  hydrogen bonds       : angle       5.10680 ( 1152)
  Misc. bond           : bond        0.00149 (    2)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 146
  time to evaluate  : 0.525 
Fit side-chains
REVERT: A  652 LYS cc_start: 0.8281 (mttp) cc_final: 0.8007 (mttp)
REVERT: B  418 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6541 (mp0)
REVERT: B  553 MET cc_start: 0.8887 (tmm) cc_final: 0.8558 (tmm)
REVERT: B  560 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.7739 (t80)
REVERT: B  573 LYS cc_start: 0.8403 (ttpp) cc_final: 0.8129 (tppt)
REVERT: B  581 SER cc_start: 0.6919 (m) cc_final: 0.6194 (m)
REVERT: D   81 GLU cc_start: 0.8128 (mp0) cc_final: 0.7664 (mp0)
REVERT: E  275 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.6935 (tmt170)
  outliers start: 22
  outliers final: 14
  residues processed: 164
  average time/residue: 0.1178
  time to fit residues: 27.6947
Evaluate side-chains
  156 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  309 THR
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  487 THR
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain B residue  100 ASN
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  418 GLU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  476 MET
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  560 PHE
Chi-restraints excluded: chain C residue   58 CYS
Chi-restraints excluded: chain E residue  275 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 34 optimal weight:    0.5980
   chunk 84 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 106 optimal weight:    0.4980
   chunk 98 optimal weight:    1.9990
   chunk 105 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 523 GLN
B 100 ASN
B 118 GLN
D  84 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.157164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.123775 restraints weight = 14337.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.127979 restraints weight = 9664.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.130787 restraints weight = 5969.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.131355 restraints weight = 4526.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.131945 restraints weight = 4709.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  12268  Z= 0.110
  Angle     :  0.554   8.912  16505  Z= 0.281
  Chirality :  0.042   0.179   1812
  Planarity :  0.003   0.042   2105
  Dihedral  :  7.447 166.226   1619
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 12.62 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.56 (0.22), residues: 1461
  helix:  0.19 (0.25), residues: 497
  sheet: -1.54 (0.29), residues: 301
  loop : -1.69 (0.22), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 338 
 TYR   0.009   0.001   TYR A 373 
 PHE   0.010   0.001   PHE A  32 
 TRP   0.021   0.001   TRP B 157 
 HIS   0.003   0.001   HIS B 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (12266)
  covalent geometry    : angle       0.55408 (16505)
  hydrogen bonds       : bond        0.03463 (  427)
  hydrogen bonds       : angle       4.89694 ( 1152)
  Misc. bond           : bond        0.00090 (    2)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 149
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
REVERT: B   25 MET cc_start: 0.7915 (tpp) cc_final: 0.7364 (mpp)
REVERT: B  354 LYS cc_start: 0.8526 (mttt) cc_final: 0.8297 (mttp)
REVERT: B  418 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6326 (mp0)
REVERT: B  453 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7031 (mt-10)
REVERT: B  553 MET cc_start: 0.9069 (tmm) cc_final: 0.8598 (tmm)
REVERT: B  560 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7660 (t80)
REVERT: B  573 LYS cc_start: 0.8582 (ttpp) cc_final: 0.8174 (tppt)
REVERT: B  617 MET cc_start: 0.8273 (mpp) cc_final: 0.7880 (mpp)
REVERT: D   39 SER cc_start: 0.8168 (t) cc_final: 0.7387 (p)
REVERT: D   81 GLU cc_start: 0.8084 (mp0) cc_final: 0.7526 (mp0)
REVERT: E  275 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.6763 (tmt170)
  outliers start: 27
  outliers final: 15
  residues processed: 169
  average time/residue: 0.1205
  time to fit residues: 28.7517
Evaluate side-chains
  159 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  309 THR
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  487 THR
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  418 GLU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  453 GLU
Chi-restraints excluded: chain B residue  476 MET
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  560 PHE
Chi-restraints excluded: chain C residue   58 CYS
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain E residue  275 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   chunk 85 optimal weight:    2.9990
   chunk 84 optimal weight:    0.0670
   chunk 145 optimal weight:    4.9990
   chunk 68 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   overall best weight:    1.5722

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

Flipped N/Q/H residues before XYZ refinement:
A 298 GLN
B 100 ASN
D  84 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.151202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.117167 restraints weight = 14620.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.121021 restraints weight = 10071.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.123786 restraints weight = 6361.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.124655 restraints weight = 4889.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.125305 restraints weight = 5017.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  12268  Z= 0.176
  Angle     :  0.598   6.450  16505  Z= 0.305
  Chirality :  0.044   0.153   1812
  Planarity :  0.003   0.041   2105
  Dihedral  :  6.655 105.685   1619
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 13.22 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.59 (0.22), residues: 1461
  helix:  0.16 (0.25), residues: 495
  sheet: -1.51 (0.29), residues: 298
  loop : -1.74 (0.22), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 338 
 TYR   0.013   0.001   TYR A 305 
 PHE   0.012   0.001   PHE A  32 
 TRP   0.020   0.001   TRP B 157 
 HIS   0.006   0.001   HIS B 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (12266)
  covalent geometry    : angle       0.59813 (16505)
  hydrogen bonds       : bond        0.04023 (  427)
  hydrogen bonds       : angle       4.97661 ( 1152)
  Misc. bond           : bond        0.00103 (    2)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 151
  time to evaluate  : 0.508 
Fit side-chains
REVERT: A  546 ASP cc_start: 0.7916 (t70) cc_final: 0.7066 (t70)
REVERT: A  550 LYS cc_start: 0.8446 (mptt) cc_final: 0.8142 (mmtt)
REVERT: B  418 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6453 (mp0)
REVERT: B  453 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7047 (mt-10)
REVERT: B  553 MET cc_start: 0.9100 (tmm) cc_final: 0.8584 (tmm)
REVERT: B  560 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7640 (t80)
REVERT: D   39 SER cc_start: 0.8120 (t) cc_final: 0.7322 (p)
REVERT: D   81 GLU cc_start: 0.7999 (mp0) cc_final: 0.7429 (mp0)
  outliers start: 25
  outliers final: 18
  residues processed: 166
  average time/residue: 0.1205
  time to fit residues: 28.5328
Evaluate side-chains
  164 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  309 THR
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  487 THR
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  418 GLU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  453 GLU
Chi-restraints excluded: chain B residue  476 MET
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  560 PHE
Chi-restraints excluded: chain C residue   58 CYS
Chi-restraints excluded: chain D residue   57 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 112 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 24 optimal weight:    8.9990
   chunk 76 optimal weight:    3.9990
   chunk 140 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 298 GLN
** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 GLN
D  84 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.151417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.118272 restraints weight = 14599.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.122149 restraints weight = 10056.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.124814 restraints weight = 6396.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.125243 restraints weight = 4921.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.125873 restraints weight = 5114.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  12268  Z= 0.124
  Angle     :  0.567   7.643  16505  Z= 0.287
  Chirality :  0.042   0.150   1812
  Planarity :  0.003   0.038   2105
  Dihedral  :  5.787 101.189   1615
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.59 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.45 (0.22), residues: 1461
  helix:  0.31 (0.25), residues: 497
  sheet: -1.40 (0.29), residues: 301
  loop : -1.70 (0.22), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 338 
 TYR   0.012   0.001   TYR A 305 
 PHE   0.010   0.001   PHE A  32 
 TRP   0.019   0.001   TRP B 157 
 HIS   0.003   0.001   HIS B 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (12266)
  covalent geometry    : angle       0.56736 (16505)
  hydrogen bonds       : bond        0.03455 (  427)
  hydrogen bonds       : angle       4.78543 ( 1152)
  Misc. bond           : bond        0.00038 (    2)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 0.491 
Fit side-chains
REVERT: A  546 ASP cc_start: 0.7910 (t70) cc_final: 0.7165 (t0)
REVERT: A  550 LYS cc_start: 0.8534 (mptt) cc_final: 0.8227 (mmtt)
REVERT: B   25 MET cc_start: 0.7849 (tpp) cc_final: 0.7342 (mpp)
REVERT: B  418 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6399 (mp0)
REVERT: B  453 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7046 (mt-10)
REVERT: B  553 MET cc_start: 0.9083 (tmm) cc_final: 0.8547 (tmm)
REVERT: B  560 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7621 (t80)
REVERT: B  649 LYS cc_start: 0.8443 (mmmm) cc_final: 0.8121 (mmmm)
REVERT: C   81 GLU cc_start: 0.7624 (mp0) cc_final: 0.7417 (mp0)
REVERT: D   39 SER cc_start: 0.8030 (t) cc_final: 0.7240 (p)
REVERT: D   81 GLU cc_start: 0.7925 (mp0) cc_final: 0.7334 (mp0)
REVERT: E  275 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.6871 (tmt170)
  outliers start: 24
  outliers final: 17
  residues processed: 166
  average time/residue: 0.1209
  time to fit residues: 28.6772
Evaluate side-chains
  164 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  309 THR
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  487 THR
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  418 GLU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  453 GLU
Chi-restraints excluded: chain B residue  476 MET
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  560 PHE
Chi-restraints excluded: chain C residue   58 CYS
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain E residue  275 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 22 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 81 optimal weight:    4.9990
   chunk 71 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 116 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 51 optimal weight:    5.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 298 GLN
** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.157990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.124480 restraints weight = 14149.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.130176 restraints weight = 9401.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.131449 restraints weight = 5902.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.133188 restraints weight = 4624.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.133668 restraints weight = 3910.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.2076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12268  Z= 0.112
  Angle     :  0.562  10.899  16505  Z= 0.281
  Chirality :  0.042   0.151   1812
  Planarity :  0.003   0.038   2105
  Dihedral  :  5.552  98.297   1615
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 13.52 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.22 (0.22), residues: 1461
  helix:  0.47 (0.25), residues: 487
  sheet: -1.19 (0.30), residues: 302
  loop : -1.55 (0.23), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 338 
 TYR   0.011   0.001   TYR A 305 
 PHE   0.012   0.001   PHE C  16 
 TRP   0.019   0.001   TRP B 157 
 HIS   0.003   0.001   HIS A 625 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (12266)
  covalent geometry    : angle       0.56160 (16505)
  hydrogen bonds       : bond        0.03305 (  427)
  hydrogen bonds       : angle       4.70385 ( 1152)
  Misc. bond           : bond        0.00026 (    2)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 152
  time to evaluate  : 0.523 
Fit side-chains
REVERT: A  546 ASP cc_start: 0.7892 (t70) cc_final: 0.7126 (t0)
REVERT: A  550 LYS cc_start: 0.8568 (mptt) cc_final: 0.8181 (mmtt)
REVERT: A  658 LEU cc_start: 0.7346 (tt) cc_final: 0.7128 (tp)
REVERT: B   25 MET cc_start: 0.7898 (tpp) cc_final: 0.7406 (mpp)
REVERT: B  100 ASN cc_start: 0.7680 (OUTLIER) cc_final: 0.7465 (t0)
REVERT: B  418 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6328 (mp0)
REVERT: B  424 GLU cc_start: 0.8250 (tm-30) cc_final: 0.8020 (tm-30)
REVERT: B  453 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7006 (mt-10)
REVERT: B  553 MET cc_start: 0.9052 (tmm) cc_final: 0.8530 (tmm)
REVERT: B  560 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7617 (t80)
REVERT: B  649 LYS cc_start: 0.8449 (mmmm) cc_final: 0.8139 (mmmm)
REVERT: C    7 LYS cc_start: 0.7655 (mttt) cc_final: 0.7414 (mttm)
REVERT: C   81 GLU cc_start: 0.7609 (mp0) cc_final: 0.7390 (mp0)
REVERT: D   39 SER cc_start: 0.8042 (t) cc_final: 0.7261 (p)
REVERT: D   81 GLU cc_start: 0.8011 (mp0) cc_final: 0.7456 (mp0)
REVERT: E  275 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.6942 (tmt170)
  outliers start: 26
  outliers final: 18
  residues processed: 170
  average time/residue: 0.1235
  time to fit residues: 29.6793
Evaluate side-chains
  168 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 145
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  309 THR
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  487 THR
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain B residue  100 ASN
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  418 GLU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  453 GLU
Chi-restraints excluded: chain B residue  476 MET
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  560 PHE
Chi-restraints excluded: chain C residue   58 CYS
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain E residue  275 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 109 optimal weight:    4.9990
   chunk 48 optimal weight:    8.9990
   chunk 112 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 90 optimal weight:    0.8980
   chunk 126 optimal weight:    3.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.153593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.121519 restraints weight = 14313.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.125255 restraints weight = 9814.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.129401 restraints weight = 6448.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.129455 restraints weight = 4932.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.130113 restraints weight = 4261.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.2109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032  12268  Z= 0.190
  Angle     :  0.625   8.274  16505  Z= 0.315
  Chirality :  0.044   0.173   1812
  Planarity :  0.003   0.037   2105
  Dihedral  :  5.808  94.258   1615
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 13.44 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.39 (0.22), residues: 1461
  helix:  0.29 (0.25), residues: 495
  sheet: -1.19 (0.30), residues: 298
  loop : -1.69 (0.23), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 338 
 TYR   0.014   0.001   TYR A 305 
 PHE   0.012   0.001   PHE D  38 
 TRP   0.018   0.001   TRP B 157 
 HIS   0.006   0.001   HIS B 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (12266)
  covalent geometry    : angle       0.62506 (16505)
  hydrogen bonds       : bond        0.04019 (  427)
  hydrogen bonds       : angle       4.93135 ( 1152)
  Misc. bond           : bond        0.00069 (    2)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 153
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
REVERT: A  546 ASP cc_start: 0.7842 (t70) cc_final: 0.7038 (t0)
REVERT: A  550 LYS cc_start: 0.8490 (mptt) cc_final: 0.8172 (mmtt)
REVERT: A  658 LEU cc_start: 0.7481 (tt) cc_final: 0.7194 (tp)
REVERT: B  418 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6319 (mp0)
REVERT: B  424 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7991 (tm-30)
REVERT: B  453 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7058 (mt-10)
REVERT: B  553 MET cc_start: 0.9056 (tmm) cc_final: 0.8540 (tmm)
REVERT: B  560 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7620 (t80)
REVERT: B  649 LYS cc_start: 0.8565 (mmmm) cc_final: 0.8249 (mmmm)
REVERT: C   81 GLU cc_start: 0.7630 (mp0) cc_final: 0.7396 (mp0)
REVERT: D   39 SER cc_start: 0.8050 (t) cc_final: 0.7262 (p)
REVERT: D   81 GLU cc_start: 0.8002 (mp0) cc_final: 0.7444 (mp0)
REVERT: E  275 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.6922 (tmt170)
  outliers start: 27
  outliers final: 21
  residues processed: 172
  average time/residue: 0.1332
  time to fit residues: 32.2574
Evaluate side-chains
  174 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 149
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  309 THR
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  487 THR
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  418 GLU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  453 GLU
Chi-restraints excluded: chain B residue  476 MET
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  560 PHE
Chi-restraints excluded: chain B residue  575 VAL
Chi-restraints excluded: chain B residue  684 ILE
Chi-restraints excluded: chain C residue   58 CYS
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain E residue  275 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 133 optimal weight:    0.5980
   chunk 93 optimal weight:    0.9980
   chunk 57 optimal weight:    9.9990
   chunk 22 optimal weight:    0.7980
   chunk 139 optimal weight:    3.9990
   chunk 125 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 100 ASN
** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 GLN
D  84 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.156928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.123298 restraints weight = 14336.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.127470 restraints weight = 9651.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.130282 restraints weight = 5991.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.131542 restraints weight = 4600.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.132069 restraints weight = 4688.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12268  Z= 0.123
  Angle     :  0.582   9.021  16505  Z= 0.292
  Chirality :  0.042   0.176   1812
  Planarity :  0.003   0.037   2105
  Dihedral  :  5.617  93.426   1615
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 13.97 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.19 (0.22), residues: 1461
  helix:  0.47 (0.25), residues: 489
  sheet: -1.10 (0.30), residues: 303
  loop : -1.56 (0.23), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 338 
 TYR   0.018   0.001   TYR C   9 
 PHE   0.011   0.001   PHE C  16 
 TRP   0.019   0.001   TRP B 157 
 HIS   0.003   0.001   HIS A 625 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (12266)
  covalent geometry    : angle       0.58191 (16505)
  hydrogen bonds       : bond        0.03420 (  427)
  hydrogen bonds       : angle       4.76816 ( 1152)
  Misc. bond           : bond        0.00042 (    2)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 152
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
REVERT: A  546 ASP cc_start: 0.7862 (t70) cc_final: 0.7075 (t0)
REVERT: A  550 LYS cc_start: 0.8451 (mptt) cc_final: 0.8170 (mmtt)
REVERT: A  658 LEU cc_start: 0.7360 (tt) cc_final: 0.7070 (tp)
REVERT: B   25 MET cc_start: 0.7893 (tpp) cc_final: 0.7435 (mpp)
REVERT: B  418 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6422 (mp0)
REVERT: B  453 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7025 (mt-10)
REVERT: B  553 MET cc_start: 0.9056 (tmm) cc_final: 0.8537 (tmm)
REVERT: B  560 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7614 (t80)
REVERT: B  649 LYS cc_start: 0.8536 (mmmm) cc_final: 0.8301 (mmmm)
REVERT: C   81 GLU cc_start: 0.7670 (mp0) cc_final: 0.7406 (mp0)
REVERT: D   39 SER cc_start: 0.8018 (t) cc_final: 0.7246 (p)
REVERT: D   81 GLU cc_start: 0.7935 (mp0) cc_final: 0.7387 (mp0)
REVERT: E  275 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.6917 (tmt170)
  outliers start: 25
  outliers final: 18
  residues processed: 169
  average time/residue: 0.1306
  time to fit residues: 30.8088
Evaluate side-chains
  171 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 149
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  309 THR
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  487 THR
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  418 GLU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  453 GLU
Chi-restraints excluded: chain B residue  476 MET
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  560 PHE
Chi-restraints excluded: chain B residue  575 VAL
Chi-restraints excluded: chain B residue  684 ILE
Chi-restraints excluded: chain C residue   58 CYS
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain E residue  275 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0980
   chunk 143 optimal weight:    0.1980
   chunk 102 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 107 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   chunk 108 optimal weight:    2.9990
   chunk 119 optimal weight:   10.0000
   overall best weight:    0.6586

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

Flipped N/Q/H residues before XYZ refinement:
** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.158189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.124640 restraints weight = 14218.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.128870 restraints weight = 9518.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.131702 restraints weight = 5910.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.133279 restraints weight = 4515.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.133750 restraints weight = 4578.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.2225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12268  Z= 0.108
  Angle     :  0.574   8.701  16505  Z= 0.286
  Chirality :  0.042   0.151   1812
  Planarity :  0.003   0.038   2105
  Dihedral  :  5.457  91.621   1615
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 14.04 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (0.22), residues: 1461
  helix:  0.52 (0.25), residues: 490
  sheet: -1.02 (0.30), residues: 309
  loop : -1.46 (0.24), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 338 
 TYR   0.017   0.001   TYR C   9 
 PHE   0.011   0.001   PHE C  16 
 TRP   0.020   0.001   TRP B 157 
 HIS   0.003   0.001   HIS A 625 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (12266)
  covalent geometry    : angle       0.57418 (16505)
  hydrogen bonds       : bond        0.03154 (  427)
  hydrogen bonds       : angle       4.63682 ( 1152)
  Misc. bond           : bond        0.00017 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1846.20 seconds
wall clock time: 32 minutes 45.04 seconds (1965.04 seconds total)