Starting phenix.real_space_refine
on Mon Jun  9 03:50:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wk7_32561/06_2025/7wk7_32561.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wk7_32561/06_2025/7wk7_32561.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wk7_32561/06_2025/7wk7_32561.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wk7_32561/06_2025/7wk7_32561.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wk7_32561/06_2025/7wk7_32561.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wk7_32561/06_2025/7wk7_32561.cif"
  }
  resolution = 3.49
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.019
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: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    6658      2.51       5
     N    1684      2.21       5
     O    1822      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 10206
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5099
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 665, 5099
          Classifications: {'peptide': 665}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 26, 'TRANS': 638}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 30
    Chain: "B"
      Number of atoms: 5099
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 665, 5099
          Classifications: {'peptide': 665}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 26, 'TRANS': 638}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 30
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'BCT': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'BCT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.30, per 1000 atoms: 0.62
  Number of scatterers: 10206
  At special positions: 0
  Unit cell: (86.818, 127.612, 118.198, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    1822      8.00
     N    1684      7.00
     C    6658      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.39
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2472

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 9 sheets defined
      66.5% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 34
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 57 through 69
      removed outlier: 3.609A  pdb=" N   ALA A  61 " --> pdb=" O   SER A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 75
      removed outlier: 3.849A  pdb=" N   TRP A  74 " --> pdb=" O   PRO A  70 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU A  75 " --> pdb=" O   ILE A  71 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 70 through 75'
    Processing helix  chain 'A' and resid 79 through 106
      removed outlier: 4.950A  pdb=" N   LEU A  85 " --> pdb=" O   LYS A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 120
      removed outlier: 3.968A  pdb=" N   GLY A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU A 117 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 127
    Processing helix  chain 'A' and resid 141 through 156
    Processing helix  chain 'A' and resid 157 through 161
      removed outlier: 3.786A  pdb=" N   HIS A 160 " --> pdb=" O   PRO A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 206
      removed outlier: 3.935A  pdb=" N   ALA A 184 " --> pdb=" O   THR A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 215
      removed outlier: 3.508A  pdb=" N   VAL A 212 " --> pdb=" O   GLY A 209 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   TYR A 214 " --> pdb=" O   ILE A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 241
    Processing helix  chain 'A' and resid 251 through 263
    Processing helix  chain 'A' and resid 268 through 292
    Processing helix  chain 'A' and resid 301 through 317
      removed outlier: 3.777A  pdb=" N   ALA A 317 " --> pdb=" O   ILE A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 374
    Processing helix  chain 'A' and resid 380 through 397
      removed outlier: 3.716A  pdb=" N   GLU A 384 " --> pdb=" O   ASP A 380 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   PHE A 397 " --> pdb=" O   VAL A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 416
      removed outlier: 3.901A  pdb=" N   GLN A 413 " --> pdb=" O   ARG A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 437
      removed outlier: 3.610A  pdb=" N   ILE A 430 " --> pdb=" O   ILE A 426 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   VAL A 431 " --> pdb=" O   SER A 427 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   VAL A 436 " --> pdb=" O   MET A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 457
      removed outlier: 3.826A  pdb=" N   LEU A 450 " --> pdb=" O   GLN A 446 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   VAL A 453 " --> pdb=" O   VAL A 449 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   VAL A 454 " --> pdb=" O   LEU A 450 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   ILE A 455 " --> pdb=" O   ALA A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 463
    Processing helix  chain 'A' and resid 464 through 466
      No H-bonds generated for 'chain 'A' and resid 464 through 466'
    Processing helix  chain 'A' and resid 467 through 474
      removed outlier: 3.676A  pdb=" N   LYS A 473 " --> pdb=" O   PRO A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 492
      removed outlier: 3.786A  pdb=" N   ILE A 490 " --> pdb=" O   CYS A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 515
      removed outlier: 3.581A  pdb=" N   LEU A 498 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU A 499 " --> pdb=" O   ASP A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 571
    Processing helix  chain 'A' and resid 573 through 595
      removed outlier: 3.834A  pdb=" N   TYR A 578 " --> pdb=" O   ALA A 574 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ARG A 586 " --> pdb=" O   LEU A 582 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   ARG A 587 " --> pdb=" O   LYS A 583 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ILE A 588 " --> pdb=" O   ALA A 584 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LYS A 590 " --> pdb=" O   ARG A 586 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE A 592 " --> pdb=" O   ILE A 588 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   LYS A 593 " --> pdb=" O   GLN A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 686
      removed outlier: 4.131A  pdb=" N   SER A 675 " --> pdb=" O   VAL A 671 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ILE A 686 " --> pdb=" O   GLU A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 696 through 706
      removed outlier: 3.624A  pdb=" N   LYS A 702 " --> pdb=" O   ASP A 698 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLN A 705 " --> pdb=" O   GLU A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 718
      removed outlier: 3.507A  pdb=" N   ARG A 717 " --> pdb=" O   ARG A 714 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 736
      removed outlier: 3.824A  pdb=" N   ALA A 725 " --> pdb=" O   THR A 721 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ILE A 726 " --> pdb=" O   VAL A 722 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 45 through 54
      removed outlier: 3.805A  pdb=" N   LEU B  50 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ALA B  51 " --> pdb=" O   ARG B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 69
      removed outlier: 3.606A  pdb=" N   ALA B  61 " --> pdb=" O   SER B  57 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL B  65 " --> pdb=" O   ALA B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 75
      removed outlier: 3.892A  pdb=" N   TRP B  74 " --> pdb=" O   PRO B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 105
      removed outlier: 3.633A  pdb=" N   LEU B  84 " --> pdb=" O   VAL B  80 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   LEU B  85 " --> pdb=" O   LYS B  81 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   SER B  86 " --> pdb=" O   GLU B  82 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ILE B  89 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL B  92 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   MET B 103 " --> pdb=" O   THR B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 110
    Processing helix  chain 'B' and resid 113 through 119
      removed outlier: 3.920A  pdb=" N   LEU B 117 " --> pdb=" O   VAL B 113 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   TYR B 118 " --> pdb=" O   GLN B 114 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   SER B 119 " --> pdb=" O   PHE B 115 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 113 through 119'
    Processing helix  chain 'B' and resid 121 through 127
    Processing helix  chain 'B' and resid 141 through 156
      removed outlier: 3.685A  pdb=" N   VAL B 151 " --> pdb=" O   MET B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 161
      removed outlier: 3.685A  pdb=" N   HIS B 160 " --> pdb=" O   PRO B 157 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   PHE B 161 " --> pdb=" O   ASP B 158 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 157 through 161'
    Processing helix  chain 'B' and resid 180 through 206
      removed outlier: 4.099A  pdb=" N   ALA B 184 " --> pdb=" O   THR B 180 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ARG B 185 " --> pdb=" O   ARG B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 213
      removed outlier: 3.565A  pdb=" N   VAL B 212 " --> pdb=" O   GLY B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 241
      removed outlier: 3.627A  pdb=" N   PHE B 229 " --> pdb=" O   THR B 225 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ILE B 238 " --> pdb=" O   SER B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 263
    Processing helix  chain 'B' and resid 268 through 292
      removed outlier: 3.617A  pdb=" N   ALA B 274 " --> pdb=" O   ALA B 270 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   THR B 278 " --> pdb=" O   ALA B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 317
      removed outlier: 3.727A  pdb=" N   THR B 307 " --> pdb=" O   GLU B 303 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ALA B 317 " --> pdb=" O   ILE B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 374
      removed outlier: 3.941A  pdb=" N   SER B 355 " --> pdb=" O   ALA B 351 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   TYR B 361 " --> pdb=" O   ALA B 357 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LYS B 374 " --> pdb=" O   VAL B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 397
      removed outlier: 3.993A  pdb=" N   GLU B 384 " --> pdb=" O   ASP B 380 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   PHE B 385 " --> pdb=" O   GLY B 381 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ILE B 386 " --> pdb=" O   ASN B 382 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   PHE B 397 " --> pdb=" O   VAL B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 416
      removed outlier: 3.552A  pdb=" N   VAL B 412 " --> pdb=" O   SER B 408 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   GLN B 413 " --> pdb=" O   ARG B 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 437
      removed outlier: 3.539A  pdb=" N   VAL B 431 " --> pdb=" O   SER B 427 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL B 436 " --> pdb=" O   MET B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 457
      removed outlier: 3.808A  pdb=" N   LEU B 450 " --> pdb=" O   GLN B 446 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   VAL B 454 " --> pdb=" O   LEU B 450 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ILE B 455 " --> pdb=" O   ALA B 451 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ASN B 457 " --> pdb=" O   VAL B 453 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 463
    Processing helix  chain 'B' and resid 464 through 466
      No H-bonds generated for 'chain 'B' and resid 464 through 466'
    Processing helix  chain 'B' and resid 467 through 474
      removed outlier: 3.651A  pdb=" N   LYS B 473 " --> pdb=" O   PRO B 469 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 475 through 492
      removed outlier: 3.770A  pdb=" N   ILE B 490 " --> pdb=" O   CYS B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 494 through 515
      removed outlier: 3.564A  pdb=" N   LEU B 498 " --> pdb=" O   LEU B 494 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU B 499 " --> pdb=" O   ASP B 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 558 through 571
      removed outlier: 3.612A  pdb=" N   LYS B 563 " --> pdb=" O   VAL B 559 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLY B 571 " --> pdb=" O   ASN B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 595
      removed outlier: 3.885A  pdb=" N   TYR B 578 " --> pdb=" O   ALA B 574 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   ARG B 587 " --> pdb=" O   LYS B 583 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ILE B 588 " --> pdb=" O   ALA B 584 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LYS B 590 " --> pdb=" O   ARG B 586 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE B 592 " --> pdb=" O   ILE B 588 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   LYS B 593 " --> pdb=" O   GLN B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 669 through 686
      removed outlier: 4.855A  pdb=" N   SER B 675 " --> pdb=" O   VAL B 671 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ILE B 686 " --> pdb=" O   GLU B 682 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 706
      removed outlier: 3.824A  pdb=" N   LYS B 702 " --> pdb=" O   ASP B 698 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   GLN B 705 " --> pdb=" O   GLU B 701 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 714 through 718
      removed outlier: 3.525A  pdb=" N   ARG B 717 " --> pdb=" O   ARG B 714 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 721 through 736
      removed outlier: 3.820A  pdb=" N   ALA B 725 " --> pdb=" O   THR B 721 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ILE B 726 " --> pdb=" O   VAL B 722 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 25
      removed outlier: 3.545A  pdb=" N   VAL B  22 " --> pdb=" O   VAL A  22 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139
    Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 164
      removed outlier: 3.995A  pdb=" N   VAL A 163 " --> pdb=" O   THR A 175 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   THR A 175 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 522 through 523
    Processing sheet with id=AA5, first strand: chain 'A' and resid 545 through 549
      removed outlier: 6.573A  pdb=" N   LYS A 546 " --> pdb=" O   VAL A 659 " (cutoff:3.500A)
      removed outlier: 7.254A  pdb=" N   ASP A 661 " --> pdb=" O   LYS A 546 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   LEU A 548 " --> pdb=" O   ASP A 661 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139
    Processing sheet with id=AA7, first strand: chain 'B' and resid 163 through 164
      removed outlier: 4.235A  pdb=" N   VAL B 163 " --> pdb=" O   THR B 175 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   THR B 175 " --> pdb=" O   VAL B 163 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 522 through 523
    Processing sheet with id=AA9, first strand: chain 'B' and resid 545 through 549
      removed outlier: 6.556A  pdb=" N   LYS B 546 " --> pdb=" O   VAL B 659 " (cutoff:3.500A)
      removed outlier: 7.319A  pdb=" N   ASP B 661 " --> pdb=" O   LYS B 546 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   LEU B 548 " --> pdb=" O   ASP B 661 " (cutoff:3.500A)

    562 hydrogen bonds defined for protein.
    1650 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.86

  Time building geometry restraints manager: 2.83 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3203
        1.34 -     1.46: 1355
        1.46 -     1.57: 5784
        1.57 -     1.69: 0
        1.69 -     1.81: 64
  Bond restraints: 10406
  Sorted by residual:
  bond pdb=" C   BCT B 800 "
       pdb=" O3  BCT B 800 "
    ideal  model  delta    sigma   weight residual
    1.389  1.436 -0.047 2.00e-02 2.50e+03 5.50e+00
  bond pdb=" C   BCT A 800 "
       pdb=" O3  BCT A 800 "
    ideal  model  delta    sigma   weight residual
    1.389  1.435 -0.046 2.00e-02 2.50e+03 5.34e+00
  bond pdb=" C   VAL B 653 "
       pdb=" N   PRO B 654 "
    ideal  model  delta    sigma   weight residual
    1.334  1.355 -0.021 2.34e-02 1.83e+03 8.24e-01
  bond pdb=" C   VAL A 653 "
       pdb=" N   PRO A 654 "
    ideal  model  delta    sigma   weight residual
    1.334  1.354 -0.021 2.34e-02 1.83e+03 7.75e-01
  bond pdb=" N   ASN A 167 "
       pdb=" CA  ASN A 167 "
    ideal  model  delta    sigma   weight residual
    1.457  1.468 -0.010 1.29e-02 6.01e+03 6.27e-01
  ... (remaining 10401 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.01: 13718
        1.01 -     2.02: 308
        2.02 -     3.03: 69
        3.03 -     4.04: 29
        4.04 -     5.05: 18
  Bond angle restraints: 14142
  Sorted by residual:
  angle pdb=" C   ARG B  79 "
        pdb=" N   VAL B  80 "
        pdb=" CA  VAL B  80 "
      ideal   model   delta    sigma   weight residual
     120.62  124.97   -4.35 1.64e+00 3.72e-01 7.03e+00
  angle pdb=" N   LEU A 521 "
        pdb=" CA  LEU A 521 "
        pdb=" C   LEU A 521 "
      ideal   model   delta    sigma   weight residual
     110.42  113.96   -3.54 1.46e+00 4.69e-01 5.86e+00
  angle pdb=" N   LEU B 521 "
        pdb=" CA  LEU B 521 "
        pdb=" C   LEU B 521 "
      ideal   model   delta    sigma   weight residual
     110.42  113.93   -3.51 1.46e+00 4.69e-01 5.79e+00
  angle pdb=" C   ALA B 434 "
        pdb=" N   ILE B 435 "
        pdb=" CA  ILE B 435 "
      ideal   model   delta    sigma   weight residual
     122.66  120.34    2.32 9.70e-01 1.06e+00 5.71e+00
  angle pdb=" C   GLY A 520 "
        pdb=" N   LEU A 521 "
        pdb=" CA  LEU A 521 "
      ideal   model   delta    sigma   weight residual
     121.56  125.25   -3.69 1.56e+00 4.11e-01 5.59e+00
  ... (remaining 14137 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.24: 5994
       17.24 -    34.49: 153
       34.49 -    51.73: 24
       51.73 -    68.97: 3
       68.97 -    86.22: 8
  Dihedral angle restraints: 6182
    sinusoidal: 2346
      harmonic: 3836
  Sorted by residual:
  dihedral pdb=" N   LEU A 496 "
           pdb=" CA  LEU A 496 "
           pdb=" CB  LEU A 496 "
           pdb=" CG  LEU A 496 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -123.81  -56.19     3      1.50e+01 4.44e-03 9.39e+00
  dihedral pdb=" CB  GLU A 303 "
           pdb=" CG  GLU A 303 "
           pdb=" CD  GLU A 303 "
           pdb=" OE1 GLU A 303 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -82.21   82.21     1      3.00e+01 1.11e-03 9.22e+00
  dihedral pdb=" N   LEU B 727 "
           pdb=" CA  LEU B 727 "
           pdb=" CB  LEU B 727 "
           pdb=" CG  LEU B 727 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -127.36  -52.64     3      1.50e+01 4.44e-03 9.13e+00
  ... (remaining 6179 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 975
       0.026 -    0.052: 469
       0.052 -    0.077: 181
       0.077 -    0.103: 75
       0.103 -    0.129: 18
  Chirality restraints: 1718
  Sorted by residual:
  chirality pdb=" CA  PRO B 553 "
            pdb=" N   PRO B 553 "
            pdb=" C   PRO B 553 "
            pdb=" CB  PRO B 553 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.16e-01
  chirality pdb=" CA  PRO A 553 "
            pdb=" N   PRO A 553 "
            pdb=" C   PRO A 553 "
            pdb=" CB  PRO A 553 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.09e-01
  chirality pdb=" CA  LEU A 668 "
            pdb=" N   LEU A 668 "
            pdb=" C   LEU A 668 "
            pdb=" CB  LEU A 668 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.86e-01
  ... (remaining 1715 not shown)

  Planarity restraints: 1760
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 552 "    0.021 5.00e-02 4.00e+02   3.14e-02 1.57e+00
        pdb=" N   PRO B 553 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO B 553 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 553 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 552 "    0.020 5.00e-02 4.00e+02   3.04e-02 1.48e+00
        pdb=" N   PRO A 553 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 553 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 553 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 300 "    0.020 5.00e-02 4.00e+02   2.99e-02 1.43e+00
        pdb=" N   PRO B 301 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO B 301 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 301 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1757 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 1077
        2.74 -     3.28: 10847
        3.28 -     3.82: 16622
        3.82 -     4.36: 19625
        4.36 -     4.90: 33392
  Nonbonded interactions: 81563
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  78 "
            pdb=" OD2 ASP A  87 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OG  SER A  90 "
            pdb=" O   GLY A 417 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OD1 ASN B 475 "
            pdb=" OG1 THR B 477 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OD1 ASN A 475 "
            pdb=" OG1 THR A 477 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   THR A 485 "
            pdb=" OG  SER A 489 "
     model   vdw
     2.237 3.040
  ... (remaining 81558 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.030
  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:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.660
  Find NCS groups from input model:        0.500
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
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      :  0.002   0.047  10406  Z= 0.093
  Angle     :  0.440   5.051  14142  Z= 0.246
  Chirality :  0.037   0.129   1718
  Planarity :  0.003   0.031   1760
  Dihedral  :  8.683  86.216   3710
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.54 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  :  5.17 %
    Favored  : 91.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.90 (0.18), residues: 1322
  helix: -2.07 (0.14), residues: 838
  sheet: -4.06 (0.61), residues: 34
  loop : -3.22 (0.25), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP A  83 
 HIS   0.001   0.000   HIS B 656 
 PHE   0.009   0.001   PHE B 555 
 TYR   0.009   0.001   TYR A 127 
 ARG   0.001   0.000   ARG A 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23070 (  562)
  hydrogen bonds       : angle       6.98527 ( 1650)
  covalent geometry    : bond        0.00176 (10406)
  covalent geometry    : angle       0.43952 (14142)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  473 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 438
  time to evaluate  : 1.021 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ASP cc_start: 0.8008 (t70) cc_final: 0.7682 (p0)
REVERT: A  195 LEU cc_start: 0.8361 (tp) cc_final: 0.8161 (tp)
REVERT: A  213 ARG cc_start: 0.7653 (mtt180) cc_final: 0.7424 (mtm-85)
REVERT: A  236 LEU cc_start: 0.8466 (tp) cc_final: 0.8144 (tt)
REVERT: A  237 LYS cc_start: 0.8670 (ttpp) cc_final: 0.8377 (tttt)
REVERT: A  244 THR cc_start: 0.8102 (p) cc_final: 0.7341 (p)
REVERT: A  245 LYS cc_start: 0.7687 (ttmm) cc_final: 0.7344 (ttmm)
REVERT: A  247 TYR cc_start: 0.7572 (m-10) cc_final: 0.6639 (m-10)
REVERT: A  262 GLN cc_start: 0.7474 (mt0) cc_final: 0.7184 (mt0)
REVERT: A  276 LEU cc_start: 0.8432 (tp) cc_final: 0.7941 (tt)
REVERT: A  280 ILE cc_start: 0.8409 (mt) cc_final: 0.8033 (mm)
REVERT: A  350 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6449 (tm)
REVERT: A  361 TYR cc_start: 0.8286 (t80) cc_final: 0.8029 (t80)
REVERT: A  369 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7733 (mmtt)
REVERT: A  384 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6573 (mm-30)
REVERT: A  385 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.8005 (t80)
REVERT: A  391 SER cc_start: 0.8553 (m) cc_final: 0.8224 (p)
REVERT: A  394 PHE cc_start: 0.8343 (t80) cc_final: 0.7437 (t80)
REVERT: A  398 PHE cc_start: 0.7707 (m-80) cc_final: 0.7392 (m-80)
REVERT: A  432 MET cc_start: 0.7318 (tpt) cc_final: 0.6933 (tpt)
REVERT: A  447 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8322 (mtpp)
REVERT: A  448 SER cc_start: 0.9040 (m) cc_final: 0.8530 (t)
REVERT: A  470 ARG cc_start: 0.7426 (tpp80) cc_final: 0.7180 (tpp80)
REVERT: A  475 ASN cc_start: 0.7165 (t0) cc_final: 0.6658 (t0)
REVERT: A  478 ASP cc_start: 0.6763 (m-30) cc_final: 0.6187 (m-30)
REVERT: A  484 PHE cc_start: 0.8603 (t80) cc_final: 0.8345 (t80)
REVERT: A  503 LEU cc_start: 0.8278 (mt) cc_final: 0.7953 (mp)
REVERT: A  556 TYR cc_start: 0.8097 (p90) cc_final: 0.7760 (p90)
REVERT: A  560 ASP cc_start: 0.7819 (m-30) cc_final: 0.6417 (m-30)
REVERT: A  563 LYS cc_start: 0.8521 (mmmt) cc_final: 0.8109 (mtpp)
REVERT: A  684 GLN cc_start: 0.8627 (tp40) cc_final: 0.8384 (tp-100)
REVERT: A  698 ASP cc_start: 0.7124 (t0) cc_final: 0.6828 (t0)
REVERT: B   71 ILE cc_start: 0.8640 (tt) cc_final: 0.8374 (tp)
REVERT: B  105 TYR cc_start: 0.8455 (m-10) cc_final: 0.8240 (m-80)
REVERT: B  160 HIS cc_start: 0.7694 (t-90) cc_final: 0.7386 (t-90)
REVERT: B  195 LEU cc_start: 0.8254 (tp) cc_final: 0.7987 (tp)
REVERT: B  207 GLN cc_start: 0.7978 (tp40) cc_final: 0.7354 (mm110)
REVERT: B  213 ARG cc_start: 0.7589 (mtt180) cc_final: 0.7183 (mtt180)
REVERT: B  244 THR cc_start: 0.7957 (p) cc_final: 0.7295 (p)
REVERT: B  247 TYR cc_start: 0.7667 (m-10) cc_final: 0.6907 (m-10)
REVERT: B  276 LEU cc_start: 0.8647 (tp) cc_final: 0.8312 (tt)
REVERT: B  277 LEU cc_start: 0.8523 (tp) cc_final: 0.8257 (tp)
REVERT: B  286 LYS cc_start: 0.8721 (tppt) cc_final: 0.8360 (ttmm)
REVERT: B  287 GLU cc_start: 0.7710 (tp30) cc_final: 0.6739 (tp30)
REVERT: B  303 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7344 (mp0)
REVERT: B  309 ILE cc_start: 0.8478 (tp) cc_final: 0.8240 (pt)
REVERT: B  311 THR cc_start: 0.7678 (p) cc_final: 0.7410 (t)
REVERT: B  355 SER cc_start: 0.8654 (m) cc_final: 0.8059 (p)
REVERT: B  366 SER cc_start: 0.8430 (t) cc_final: 0.7883 (p)
REVERT: B  377 TYR cc_start: 0.7857 (p90) cc_final: 0.7190 (p90)
REVERT: B  378 VAL cc_start: 0.8437 (t) cc_final: 0.7893 (p)
REVERT: B  391 SER cc_start: 0.8479 (m) cc_final: 0.8137 (p)
REVERT: B  394 PHE cc_start: 0.8446 (t80) cc_final: 0.7316 (t80)
REVERT: B  398 PHE cc_start: 0.7613 (m-80) cc_final: 0.7390 (m-80)
REVERT: B  414 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6769 (tm-30)
REVERT: B  422 VAL cc_start: 0.7738 (t) cc_final: 0.7268 (p)
REVERT: B  432 MET cc_start: 0.7453 (tpt) cc_final: 0.7085 (tpt)
REVERT: B  447 LYS cc_start: 0.8636 (mtpt) cc_final: 0.8307 (mtpt)
REVERT: B  448 SER cc_start: 0.9105 (m) cc_final: 0.8706 (t)
REVERT: B  473 LYS cc_start: 0.8400 (mtpt) cc_final: 0.8125 (mtpt)
REVERT: B  475 ASN cc_start: 0.7284 (t0) cc_final: 0.6543 (t0)
REVERT: B  478 ASP cc_start: 0.7002 (m-30) cc_final: 0.6217 (m-30)
REVERT: B  503 LEU cc_start: 0.8397 (mt) cc_final: 0.8103 (mp)
REVERT: B  573 ASP cc_start: 0.7590 (t0) cc_final: 0.5764 (t0)
REVERT: B  727 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7623 (mm)
  outliers start: 35
  outliers final: 9
  residues processed: 464
  average time/residue: 0.2503
  time to fit residues: 154.9432
Evaluate side-chains
  380 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 367
  time to evaluate  : 1.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 LYS
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  543 GLU
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  303 GLU
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  727 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 67 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 103 optimal weight:    0.4980
   chunk 40 optimal weight:    0.4980
   chunk 62 optimal weight:    0.5980
   chunk 77 optimal weight:    0.2980
   chunk 119 optimal weight:    0.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 135 HIS
A 382 ASN
A 656 HIS
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 446 GLN
B 464 GLN
B 474 GLN
B 731 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.123548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.104801 restraints weight = 17757.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 2.84
r_work: 0.3271 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10406  Z= 0.160
  Angle     :  0.616   9.951  14142  Z= 0.318
  Chirality :  0.043   0.188   1718
  Planarity :  0.005   0.038   1760
  Dihedral  :  6.068  80.160   1443
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 16.04 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.06 (0.22), residues: 1322
  helix: -0.48 (0.17), residues: 836
  sheet: -3.59 (0.74), residues: 36
  loop : -2.78 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  74 
 HIS   0.013   0.001   HIS A 656 
 PHE   0.022   0.001   PHE A 130 
 TYR   0.016   0.001   TYR A 377 
 ARG   0.007   0.001   ARG B 576 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04721 (  562)
  hydrogen bonds       : angle       4.36467 ( 1650)
  covalent geometry    : bond        0.00345 (10406)
  covalent geometry    : angle       0.61650 (14142)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  422 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 377
  time to evaluate  : 1.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 TYR cc_start: 0.7765 (m-10) cc_final: 0.7520 (m-10)
REVERT: A   48 ASP cc_start: 0.8169 (t70) cc_final: 0.7807 (p0)
REVERT: A   87 ASP cc_start: 0.7247 (m-30) cc_final: 0.6897 (t0)
REVERT: A   94 THR cc_start: 0.8263 (m) cc_final: 0.7880 (p)
REVERT: A  195 LEU cc_start: 0.8550 (tp) cc_final: 0.8286 (tp)
REVERT: A  236 LEU cc_start: 0.8705 (tp) cc_final: 0.8201 (tt)
REVERT: A  237 LYS cc_start: 0.8594 (ttpp) cc_final: 0.8394 (ttpt)
REVERT: A  244 THR cc_start: 0.8392 (p) cc_final: 0.8188 (t)
REVERT: A  245 LYS cc_start: 0.8185 (ttmm) cc_final: 0.7841 (ttmm)
REVERT: A  247 TYR cc_start: 0.8109 (m-10) cc_final: 0.7359 (m-10)
REVERT: A  263 ASN cc_start: 0.8546 (t0) cc_final: 0.8242 (t0)
REVERT: A  285 VAL cc_start: 0.8715 (m) cc_final: 0.8423 (p)
REVERT: A  289 ASN cc_start: 0.9034 (t0) cc_final: 0.8735 (p0)
REVERT: A  349 MET cc_start: 0.6719 (ptp) cc_final: 0.6518 (ptp)
REVERT: A  369 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7838 (mmtt)
REVERT: A  370 VAL cc_start: 0.8522 (t) cc_final: 0.8315 (p)
REVERT: A  378 VAL cc_start: 0.8250 (t) cc_final: 0.7920 (p)
REVERT: A  384 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7134 (mm-30)
REVERT: A  385 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7887 (t80)
REVERT: A  391 SER cc_start: 0.8682 (m) cc_final: 0.8314 (p)
REVERT: A  394 PHE cc_start: 0.8581 (t80) cc_final: 0.7661 (t80)
REVERT: A  398 PHE cc_start: 0.8070 (m-80) cc_final: 0.7581 (m-80)
REVERT: A  432 MET cc_start: 0.7804 (tpt) cc_final: 0.7368 (tpt)
REVERT: A  436 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8478 (m)
REVERT: A  447 LYS cc_start: 0.8841 (mtpt) cc_final: 0.8439 (mtpp)
REVERT: A  484 PHE cc_start: 0.8724 (t80) cc_final: 0.8499 (t80)
REVERT: A  556 TYR cc_start: 0.8554 (p90) cc_final: 0.8038 (p90)
REVERT: A  560 ASP cc_start: 0.8383 (m-30) cc_final: 0.7158 (m-30)
REVERT: A  573 ASP cc_start: 0.7873 (t0) cc_final: 0.7648 (t0)
REVERT: A  581 ARG cc_start: 0.8079 (mmt180) cc_final: 0.7794 (mtp85)
REVERT: A  677 ARG cc_start: 0.8189 (ptm-80) cc_final: 0.7836 (ttt-90)
REVERT: A  698 ASP cc_start: 0.7683 (t0) cc_final: 0.7338 (t0)
REVERT: B   34 GLN cc_start: 0.8413 (mt0) cc_final: 0.8201 (mt0)
REVERT: B   66 LYS cc_start: 0.8342 (tppt) cc_final: 0.8094 (tppt)
REVERT: B   69 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8300 (mt)
REVERT: B  100 LEU cc_start: 0.9040 (tp) cc_final: 0.8764 (tp)
REVERT: B  195 LEU cc_start: 0.8555 (tp) cc_final: 0.8163 (tp)
REVERT: B  213 ARG cc_start: 0.8193 (mtt180) cc_final: 0.7666 (mtt180)
REVERT: B  244 THR cc_start: 0.8429 (p) cc_final: 0.7892 (t)
REVERT: B  259 GLU cc_start: 0.8558 (tt0) cc_final: 0.8159 (tt0)
REVERT: B  276 LEU cc_start: 0.8666 (tp) cc_final: 0.8416 (tt)
REVERT: B  287 GLU cc_start: 0.8039 (tp30) cc_final: 0.7054 (tp30)
REVERT: B  309 ILE cc_start: 0.8434 (tp) cc_final: 0.8224 (pt)
REVERT: B  355 SER cc_start: 0.8585 (m) cc_final: 0.8149 (p)
REVERT: B  361 TYR cc_start: 0.8514 (t80) cc_final: 0.8168 (t80)
REVERT: B  366 SER cc_start: 0.8559 (t) cc_final: 0.8342 (p)
REVERT: B  367 VAL cc_start: 0.8807 (t) cc_final: 0.8510 (m)
REVERT: B  370 VAL cc_start: 0.9028 (t) cc_final: 0.8797 (p)
REVERT: B  382 ASN cc_start: 0.8548 (m-40) cc_final: 0.7634 (t0)
REVERT: B  391 SER cc_start: 0.8684 (m) cc_final: 0.8369 (p)
REVERT: B  394 PHE cc_start: 0.8524 (t80) cc_final: 0.7388 (t80)
REVERT: B  398 PHE cc_start: 0.8004 (m-80) cc_final: 0.7631 (m-80)
REVERT: B  414 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7044 (tm-30)
REVERT: B  432 MET cc_start: 0.8019 (tpt) cc_final: 0.7596 (tpt)
REVERT: B  447 LYS cc_start: 0.8736 (mtpt) cc_final: 0.8431 (mtpt)
REVERT: B  473 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8337 (mtpt)
REVERT: B  587 ARG cc_start: 0.7382 (mmm160) cc_final: 0.7155 (tpt170)
REVERT: B  702 LYS cc_start: 0.8176 (tptp) cc_final: 0.7421 (ttmm)
  outliers start: 45
  outliers final: 26
  residues processed: 401
  average time/residue: 0.2745
  time to fit residues: 148.6328
Evaluate side-chains
  388 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 359
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  382 ASN
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  543 GLU
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  656 HIS
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  246 ASN
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  386 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  582 LEU
Chi-restraints excluded: chain B residue  681 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   chunk 3 optimal weight:    6.9990
   chunk 103 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 656 HIS
B 135 HIS
B 160 HIS
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.119352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.100264 restraints weight = 17950.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.83
r_work: 0.3204 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.3278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  10406  Z= 0.199
  Angle     :  0.643   9.935  14142  Z= 0.332
  Chirality :  0.044   0.204   1718
  Planarity :  0.005   0.044   1760
  Dihedral  :  5.533  80.595   1433
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 19.61 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.23), residues: 1322
  helix: -0.15 (0.17), residues: 864
  sheet: -3.25 (0.77), residues: 36
  loop : -2.47 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 472 
 HIS   0.013   0.001   HIS B 160 
 PHE   0.018   0.001   PHE B 272 
 TYR   0.014   0.001   TYR B 578 
 ARG   0.008   0.001   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04466 (  562)
  hydrogen bonds       : angle       4.19341 ( 1650)
  covalent geometry    : bond        0.00433 (10406)
  covalent geometry    : angle       0.64273 (14142)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  402 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 353
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 ASP cc_start: 0.7224 (m-30) cc_final: 0.6865 (t0)
REVERT: A  195 LEU cc_start: 0.8673 (tp) cc_final: 0.8337 (tp)
REVERT: A  236 LEU cc_start: 0.8779 (tp) cc_final: 0.8339 (tt)
REVERT: A  240 LEU cc_start: 0.8597 (mm) cc_final: 0.8344 (mp)
REVERT: A  244 THR cc_start: 0.8375 (p) cc_final: 0.8164 (p)
REVERT: A  245 LYS cc_start: 0.8245 (ttmm) cc_final: 0.7868 (ttmm)
REVERT: A  247 TYR cc_start: 0.8121 (m-10) cc_final: 0.7346 (m-10)
REVERT: A  251 LEU cc_start: 0.8867 (mm) cc_final: 0.8377 (mm)
REVERT: A  369 LYS cc_start: 0.8315 (mmtt) cc_final: 0.7975 (mmtt)
REVERT: A  384 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7157 (mm-30)
REVERT: A  385 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7875 (t80)
REVERT: A  391 SER cc_start: 0.8630 (m) cc_final: 0.8290 (p)
REVERT: A  394 PHE cc_start: 0.8526 (t80) cc_final: 0.7804 (t80)
REVERT: A  398 PHE cc_start: 0.8058 (m-80) cc_final: 0.7747 (m-80)
REVERT: A  414 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7394 (tm-30)
REVERT: A  432 MET cc_start: 0.7772 (tpt) cc_final: 0.7402 (tpt)
REVERT: A  436 VAL cc_start: 0.8776 (OUTLIER) cc_final: 0.8526 (m)
REVERT: A  447 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8383 (ttmt)
REVERT: A  470 ARG cc_start: 0.8009 (tpp80) cc_final: 0.7785 (tpp80)
REVERT: A  475 ASN cc_start: 0.7192 (m-40) cc_final: 0.6767 (m-40)
REVERT: A  478 ASP cc_start: 0.7311 (m-30) cc_final: 0.7095 (m-30)
REVERT: A  563 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8398 (mmmt)
REVERT: A  573 ASP cc_start: 0.7988 (t0) cc_final: 0.7656 (t0)
REVERT: A  581 ARG cc_start: 0.8079 (mmt180) cc_final: 0.7774 (mtp85)
REVERT: A  677 ARG cc_start: 0.8335 (ptm-80) cc_final: 0.7784 (ttt90)
REVERT: A  698 ASP cc_start: 0.7698 (t0) cc_final: 0.7331 (t0)
REVERT: B   34 GLN cc_start: 0.8392 (mt0) cc_final: 0.8174 (mt0)
REVERT: B   66 LYS cc_start: 0.8366 (tppt) cc_final: 0.8134 (tppt)
REVERT: B   69 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8343 (mt)
REVERT: B  100 LEU cc_start: 0.9046 (tp) cc_final: 0.8834 (tp)
REVERT: B  155 MET cc_start: 0.8255 (mpp) cc_final: 0.7829 (mpp)
REVERT: B  195 LEU cc_start: 0.8665 (tp) cc_final: 0.8296 (tp)
REVERT: B  207 GLN cc_start: 0.8159 (mm110) cc_final: 0.7944 (mm-40)
REVERT: B  213 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7867 (mtt180)
REVERT: B  244 THR cc_start: 0.8393 (p) cc_final: 0.7751 (t)
REVERT: B  259 GLU cc_start: 0.8473 (tt0) cc_final: 0.8074 (tt0)
REVERT: B  276 LEU cc_start: 0.8707 (tp) cc_final: 0.8500 (tt)
REVERT: B  287 GLU cc_start: 0.8086 (tp30) cc_final: 0.7112 (tp30)
REVERT: B  309 ILE cc_start: 0.8466 (tp) cc_final: 0.8236 (pt)
REVERT: B  355 SER cc_start: 0.8604 (m) cc_final: 0.8168 (p)
REVERT: B  361 TYR cc_start: 0.8609 (t80) cc_final: 0.8262 (t80)
REVERT: B  366 SER cc_start: 0.8616 (t) cc_final: 0.8350 (p)
REVERT: B  367 VAL cc_start: 0.8857 (t) cc_final: 0.8515 (m)
REVERT: B  378 VAL cc_start: 0.8582 (t) cc_final: 0.8327 (m)
REVERT: B  382 ASN cc_start: 0.8506 (m-40) cc_final: 0.7904 (t0)
REVERT: B  384 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7362 (mm-30)
REVERT: B  391 SER cc_start: 0.8680 (m) cc_final: 0.8285 (p)
REVERT: B  394 PHE cc_start: 0.8483 (t80) cc_final: 0.7444 (t80)
REVERT: B  398 PHE cc_start: 0.8010 (m-80) cc_final: 0.7720 (m-80)
REVERT: B  414 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7128 (tm-30)
REVERT: B  432 MET cc_start: 0.8052 (tpt) cc_final: 0.7656 (tpt)
REVERT: B  447 LYS cc_start: 0.8797 (mtpt) cc_final: 0.8456 (mtpt)
REVERT: B  459 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8712 (ttpp)
REVERT: B  473 LYS cc_start: 0.8519 (mtpt) cc_final: 0.8258 (mtpt)
REVERT: B  478 ASP cc_start: 0.7488 (m-30) cc_final: 0.7253 (m-30)
REVERT: B  531 LYS cc_start: 0.8524 (mmmt) cc_final: 0.7859 (mmmt)
  outliers start: 49
  outliers final: 31
  residues processed: 380
  average time/residue: 0.2873
  time to fit residues: 144.6558
Evaluate side-chains
  362 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 327
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  543 GLU
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  656 HIS
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  246 ASN
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  386 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  459 LYS
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  529 ILE
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  681 LYS
Chi-restraints excluded: chain B residue  700 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 131 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 76 optimal weight:    0.2980
   chunk 69 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   chunk 40 optimal weight:    6.9990
   chunk 117 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 103 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 382 ASN
** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 656 HIS
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.119816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.100795 restraints weight = 17750.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 2.82
r_work: 0.3205 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.3570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  10406  Z= 0.176
  Angle     :  0.624   9.879  14142  Z= 0.325
  Chirality :  0.044   0.209   1718
  Planarity :  0.004   0.045   1760
  Dihedral  :  5.606  81.612   1433
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 20.86 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.23), residues: 1322
  helix:  0.13 (0.18), residues: 856
  sheet: -3.02 (0.80), residues: 36
  loop : -2.28 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 472 
 HIS   0.005   0.001   HIS A 656 
 PHE   0.012   0.001   PHE A 484 
 TYR   0.012   0.001   TYR B  20 
 ARG   0.008   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04302 (  562)
  hydrogen bonds       : angle       4.07784 ( 1650)
  covalent geometry    : bond        0.00391 (10406)
  covalent geometry    : angle       0.62372 (14142)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  379 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 328
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 ASP cc_start: 0.7237 (m-30) cc_final: 0.6983 (t0)
REVERT: A   94 THR cc_start: 0.8443 (t) cc_final: 0.8066 (p)
REVERT: A  195 LEU cc_start: 0.8675 (tp) cc_final: 0.8378 (tp)
REVERT: A  236 LEU cc_start: 0.8778 (tp) cc_final: 0.8361 (tt)
REVERT: A  245 LYS cc_start: 0.8235 (ttmm) cc_final: 0.7920 (ttmm)
REVERT: A  247 TYR cc_start: 0.8148 (m-10) cc_final: 0.7497 (m-10)
REVERT: A  251 LEU cc_start: 0.8848 (mm) cc_final: 0.8558 (mm)
REVERT: A  254 ILE cc_start: 0.8322 (pt) cc_final: 0.8099 (pt)
REVERT: A  276 LEU cc_start: 0.8668 (tp) cc_final: 0.8408 (tp)
REVERT: A  369 LYS cc_start: 0.8270 (mmtt) cc_final: 0.7958 (mmtt)
REVERT: A  384 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7140 (mm-30)
REVERT: A  385 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7800 (t80)
REVERT: A  391 SER cc_start: 0.8673 (m) cc_final: 0.8297 (p)
REVERT: A  394 PHE cc_start: 0.8525 (t80) cc_final: 0.7895 (t80)
REVERT: A  398 PHE cc_start: 0.8003 (m-80) cc_final: 0.7713 (m-80)
REVERT: A  414 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7411 (tm-30)
REVERT: A  432 MET cc_start: 0.7804 (tpt) cc_final: 0.7443 (tpt)
REVERT: A  436 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8526 (m)
REVERT: A  447 LYS cc_start: 0.8804 (mtpt) cc_final: 0.8360 (ttmt)
REVERT: A  470 ARG cc_start: 0.8011 (tpp80) cc_final: 0.7783 (tpp80)
REVERT: A  475 ASN cc_start: 0.7318 (m-40) cc_final: 0.6975 (m-40)
REVERT: A  573 ASP cc_start: 0.7988 (t0) cc_final: 0.7658 (t0)
REVERT: A  581 ARG cc_start: 0.8085 (mmt180) cc_final: 0.7744 (mtp85)
REVERT: A  677 ARG cc_start: 0.8409 (ptm-80) cc_final: 0.7864 (ttt90)
REVERT: A  698 ASP cc_start: 0.7690 (t0) cc_final: 0.7313 (t0)
REVERT: B   71 ILE cc_start: 0.8668 (tt) cc_final: 0.8331 (tp)
REVERT: B  100 LEU cc_start: 0.9176 (tp) cc_final: 0.8964 (tp)
REVERT: B  155 MET cc_start: 0.8216 (mpp) cc_final: 0.7867 (mpp)
REVERT: B  195 LEU cc_start: 0.8658 (tp) cc_final: 0.8287 (tp)
REVERT: B  207 GLN cc_start: 0.8209 (mm110) cc_final: 0.7976 (mm110)
REVERT: B  213 ARG cc_start: 0.8203 (mtt180) cc_final: 0.7926 (mtt180)
REVERT: B  236 LEU cc_start: 0.8912 (tt) cc_final: 0.8621 (tt)
REVERT: B  244 THR cc_start: 0.8412 (p) cc_final: 0.8128 (t)
REVERT: B  247 TYR cc_start: 0.8066 (m-80) cc_final: 0.7278 (m-10)
REVERT: B  276 LEU cc_start: 0.8693 (tp) cc_final: 0.8488 (tt)
REVERT: B  287 GLU cc_start: 0.8099 (tp30) cc_final: 0.7101 (tp30)
REVERT: B  303 GLU cc_start: 0.8128 (mp0) cc_final: 0.7764 (mp0)
REVERT: B  309 ILE cc_start: 0.8520 (tp) cc_final: 0.8276 (pt)
REVERT: B  329 LYS cc_start: 0.8282 (pttt) cc_final: 0.8068 (pttt)
REVERT: B  355 SER cc_start: 0.8533 (m) cc_final: 0.8092 (p)
REVERT: B  366 SER cc_start: 0.8566 (t) cc_final: 0.8341 (p)
REVERT: B  367 VAL cc_start: 0.8768 (t) cc_final: 0.8555 (m)
REVERT: B  373 THR cc_start: 0.8528 (m) cc_final: 0.8141 (t)
REVERT: B  378 VAL cc_start: 0.8588 (t) cc_final: 0.8352 (m)
REVERT: B  382 ASN cc_start: 0.8510 (m-40) cc_final: 0.8093 (t0)
REVERT: B  384 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7468 (mm-30)
REVERT: B  391 SER cc_start: 0.8699 (m) cc_final: 0.8266 (p)
REVERT: B  394 PHE cc_start: 0.8499 (t80) cc_final: 0.7481 (t80)
REVERT: B  398 PHE cc_start: 0.8004 (m-80) cc_final: 0.7694 (m-80)
REVERT: B  432 MET cc_start: 0.8059 (tpt) cc_final: 0.7676 (tpt)
REVERT: B  447 LYS cc_start: 0.8826 (mtpt) cc_final: 0.8477 (mtpt)
REVERT: B  459 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8729 (ttpp)
REVERT: B  473 LYS cc_start: 0.8452 (mtpt) cc_final: 0.8246 (mtpt)
REVERT: B  475 ASN cc_start: 0.7644 (m-40) cc_final: 0.7387 (m-40)
REVERT: B  478 ASP cc_start: 0.7567 (m-30) cc_final: 0.7306 (m-30)
REVERT: B  531 LYS cc_start: 0.8527 (mmmt) cc_final: 0.7798 (mmmt)
REVERT: B  677 ARG cc_start: 0.8540 (tpt-90) cc_final: 0.8221 (tpt-90)
REVERT: B  681 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8352 (ttmm)
REVERT: B  702 LYS cc_start: 0.7994 (tptp) cc_final: 0.7358 (tptm)
REVERT: B  714 ARG cc_start: 0.8489 (mtm-85) cc_final: 0.8138 (mtm-85)
  outliers start: 51
  outliers final: 36
  residues processed: 357
  average time/residue: 0.2941
  time to fit residues: 139.7857
Evaluate side-chains
  374 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 334
  time to evaluate  : 1.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  543 GLU
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  703 MET
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  246 ASN
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  386 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  459 LYS
Chi-restraints excluded: chain B residue  529 ILE
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  681 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 92 optimal weight:    0.6980
   chunk 109 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0980
   chunk 63 optimal weight:    0.6980
   chunk 57 optimal weight:    5.9990
   chunk 64 optimal weight:    0.6980
   chunk 121 optimal weight:    0.7980
   chunk 122 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0170
   overall best weight:    0.4218

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
A 382 ASN
A 457 ASN
** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 656 HIS
B  34 GLN
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.120374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.101225 restraints weight = 17609.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.81
r_work: 0.3218 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.3723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10406  Z= 0.144
  Angle     :  0.628   9.762  14142  Z= 0.319
  Chirality :  0.043   0.169   1718
  Planarity :  0.004   0.046   1760
  Dihedral  :  5.636  82.481   1433
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 22.10 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.23), residues: 1322
  helix:  0.35 (0.18), residues: 850
  sheet: -2.58 (0.85), residues: 36
  loop : -2.24 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 472 
 HIS   0.013   0.001   HIS A 656 
 PHE   0.013   0.001   PHE A 115 
 TYR   0.010   0.001   TYR B 578 
 ARG   0.013   0.001   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04038 (  562)
  hydrogen bonds       : angle       3.99600 ( 1650)
  covalent geometry    : bond        0.00322 (10406)
  covalent geometry    : angle       0.62814 (14142)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  382 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 328
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8566 (t)
REVERT: A   36 ARG cc_start: 0.8138 (tpp-160) cc_final: 0.7546 (mpp-170)
REVERT: A   87 ASP cc_start: 0.7239 (m-30) cc_final: 0.6876 (t0)
REVERT: A   94 THR cc_start: 0.8445 (t) cc_final: 0.8081 (p)
REVERT: A  195 LEU cc_start: 0.8650 (tp) cc_final: 0.8375 (tp)
REVERT: A  213 ARG cc_start: 0.8237 (mtm180) cc_final: 0.8021 (ttm170)
REVERT: A  236 LEU cc_start: 0.8790 (tp) cc_final: 0.8442 (tt)
REVERT: A  245 LYS cc_start: 0.8289 (ttmm) cc_final: 0.7916 (ttmm)
REVERT: A  247 TYR cc_start: 0.8197 (m-10) cc_final: 0.7607 (m-10)
REVERT: A  251 LEU cc_start: 0.8703 (mm) cc_final: 0.8369 (mm)
REVERT: A  254 ILE cc_start: 0.8374 (pt) cc_final: 0.8122 (pt)
REVERT: A  276 LEU cc_start: 0.8659 (tp) cc_final: 0.8394 (tp)
REVERT: A  384 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7178 (mm-30)
REVERT: A  385 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7799 (t80)
REVERT: A  391 SER cc_start: 0.8678 (m) cc_final: 0.8325 (p)
REVERT: A  414 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7410 (tm-30)
REVERT: A  432 MET cc_start: 0.7795 (tpt) cc_final: 0.7435 (tpt)
REVERT: A  436 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8494 (m)
REVERT: A  447 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8456 (mtpt)
REVERT: A  470 ARG cc_start: 0.7992 (tpp80) cc_final: 0.7761 (tpp80)
REVERT: A  475 ASN cc_start: 0.7343 (t0) cc_final: 0.6934 (m-40)
REVERT: A  478 ASP cc_start: 0.7418 (m-30) cc_final: 0.7213 (m-30)
REVERT: A  563 LYS cc_start: 0.8830 (mmmt) cc_final: 0.8449 (mmmt)
REVERT: A  573 ASP cc_start: 0.7978 (t0) cc_final: 0.7619 (t0)
REVERT: A  581 ARG cc_start: 0.8069 (mmt180) cc_final: 0.7719 (mtp85)
REVERT: A  677 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7993 (ttt-90)
REVERT: A  698 ASP cc_start: 0.7655 (t0) cc_final: 0.7273 (t0)
REVERT: A  704 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7792 (tm-30)
REVERT: B   71 ILE cc_start: 0.8655 (tt) cc_final: 0.8336 (tp)
REVERT: B  100 LEU cc_start: 0.9171 (tp) cc_final: 0.8930 (tp)
REVERT: B  155 MET cc_start: 0.8258 (mpp) cc_final: 0.7951 (mpp)
REVERT: B  195 LEU cc_start: 0.8639 (tp) cc_final: 0.8291 (tp)
REVERT: B  207 GLN cc_start: 0.8205 (mm110) cc_final: 0.7947 (mm110)
REVERT: B  213 ARG cc_start: 0.8181 (mtt180) cc_final: 0.7897 (mtt180)
REVERT: B  236 LEU cc_start: 0.8878 (tt) cc_final: 0.8648 (tt)
REVERT: B  240 LEU cc_start: 0.8836 (mm) cc_final: 0.8505 (mp)
REVERT: B  244 THR cc_start: 0.8425 (p) cc_final: 0.8141 (t)
REVERT: B  287 GLU cc_start: 0.8100 (tp30) cc_final: 0.7103 (tp30)
REVERT: B  367 VAL cc_start: 0.8739 (t) cc_final: 0.8519 (m)
REVERT: B  373 THR cc_start: 0.8478 (m) cc_final: 0.8134 (t)
REVERT: B  382 ASN cc_start: 0.8472 (m-40) cc_final: 0.8104 (t0)
REVERT: B  391 SER cc_start: 0.8701 (m) cc_final: 0.8274 (p)
REVERT: B  394 PHE cc_start: 0.8472 (t80) cc_final: 0.7455 (t80)
REVERT: B  398 PHE cc_start: 0.7953 (m-80) cc_final: 0.7643 (m-80)
REVERT: B  432 MET cc_start: 0.7980 (tpt) cc_final: 0.7581 (tpt)
REVERT: B  447 LYS cc_start: 0.8806 (mtpt) cc_final: 0.8429 (mtpt)
REVERT: B  473 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8284 (mtpt)
REVERT: B  478 ASP cc_start: 0.7664 (m-30) cc_final: 0.7406 (m-30)
REVERT: B  563 LYS cc_start: 0.8790 (mmmt) cc_final: 0.8581 (mmmm)
REVERT: B  677 ARG cc_start: 0.8554 (tpt-90) cc_final: 0.8286 (tpt-90)
REVERT: B  681 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8322 (ttmm)
REVERT: B  702 LYS cc_start: 0.7931 (tptp) cc_final: 0.7232 (tptp)
REVERT: B  714 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.8127 (mtm-85)
  outliers start: 54
  outliers final: 36
  residues processed: 361
  average time/residue: 0.2700
  time to fit residues: 129.8449
Evaluate side-chains
  357 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 316
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  457 ASN
Chi-restraints excluded: chain A residue  543 GLU
Chi-restraints excluded: chain A residue  580 LYS
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  677 ARG
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  246 ASN
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  681 LYS
Chi-restraints excluded: chain B residue  697 ASP
Chi-restraints excluded: chain B residue  700 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0870
   chunk 22 optimal weight:    0.9990
   chunk 73 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 106 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 113 optimal weight:    0.1980
   chunk 4 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
A  33 GLN
A  34 GLN
A 135 HIS
A 382 ASN
** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 656 HIS
B  34 GLN
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.120871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.101775 restraints weight = 17970.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 2.89
r_work: 0.3219 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.3882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10406  Z= 0.147
  Angle     :  0.625   9.781  14142  Z= 0.317
  Chirality :  0.043   0.181   1718
  Planarity :  0.004   0.043   1760
  Dihedral  :  5.595  82.823   1431
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 22.46 %
    Favored  : 72.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.24), residues: 1322
  helix:  0.46 (0.18), residues: 852
  sheet: -2.20 (0.91), residues: 36
  loop : -2.15 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 472 
 HIS   0.011   0.001   HIS A 656 
 PHE   0.018   0.001   PHE A 394 
 TYR   0.010   0.001   TYR B  20 
 ARG   0.010   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03964 (  562)
  hydrogen bonds       : angle       3.94665 ( 1650)
  covalent geometry    : bond        0.00330 (10406)
  covalent geometry    : angle       0.62455 (14142)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  384 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 329
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8504 (t)
REVERT: A   36 ARG cc_start: 0.8128 (tpp-160) cc_final: 0.7558 (mpp-170)
REVERT: A   48 ASP cc_start: 0.8220 (t70) cc_final: 0.7860 (p0)
REVERT: A   87 ASP cc_start: 0.7292 (m-30) cc_final: 0.6925 (t0)
REVERT: A   88 ILE cc_start: 0.7530 (mm) cc_final: 0.7280 (mm)
REVERT: A   94 THR cc_start: 0.8506 (t) cc_final: 0.8122 (p)
REVERT: A  195 LEU cc_start: 0.8597 (tp) cc_final: 0.8345 (tp)
REVERT: A  213 ARG cc_start: 0.8304 (mtm180) cc_final: 0.8081 (ttm170)
REVERT: A  236 LEU cc_start: 0.8761 (tp) cc_final: 0.8413 (tt)
REVERT: A  245 LYS cc_start: 0.8354 (ttmm) cc_final: 0.7949 (ttmm)
REVERT: A  247 TYR cc_start: 0.8188 (m-10) cc_final: 0.7561 (m-10)
REVERT: A  251 LEU cc_start: 0.8705 (mm) cc_final: 0.8365 (mm)
REVERT: A  254 ILE cc_start: 0.8457 (pt) cc_final: 0.8168 (pt)
REVERT: A  276 LEU cc_start: 0.8613 (tp) cc_final: 0.8351 (tp)
REVERT: A  369 LYS cc_start: 0.8257 (mmtt) cc_final: 0.7899 (mmtt)
REVERT: A  384 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7302 (mm-30)
REVERT: A  385 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7727 (t80)
REVERT: A  391 SER cc_start: 0.8754 (m) cc_final: 0.8376 (p)
REVERT: A  394 PHE cc_start: 0.8580 (t80) cc_final: 0.8378 (t80)
REVERT: A  414 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7460 (tm-30)
REVERT: A  432 MET cc_start: 0.7815 (tpt) cc_final: 0.7437 (tpt)
REVERT: A  436 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8523 (m)
REVERT: A  447 LYS cc_start: 0.8842 (mtpt) cc_final: 0.8422 (mtpt)
REVERT: A  470 ARG cc_start: 0.8001 (tpp80) cc_final: 0.7768 (tpp80)
REVERT: A  573 ASP cc_start: 0.7906 (t0) cc_final: 0.7559 (t0)
REVERT: A  581 ARG cc_start: 0.8025 (mmt180) cc_final: 0.7653 (mtp85)
REVERT: A  677 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8050 (ttt-90)
REVERT: A  698 ASP cc_start: 0.7680 (t0) cc_final: 0.7298 (t0)
REVERT: A  704 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7822 (tm-30)
REVERT: B   71 ILE cc_start: 0.8654 (tt) cc_final: 0.8300 (tp)
REVERT: B  100 LEU cc_start: 0.9137 (tp) cc_final: 0.8930 (tp)
REVERT: B  135 HIS cc_start: 0.7643 (m-70) cc_final: 0.7430 (m-70)
REVERT: B  155 MET cc_start: 0.8278 (mpp) cc_final: 0.7961 (mpp)
REVERT: B  195 LEU cc_start: 0.8592 (tp) cc_final: 0.8253 (tp)
REVERT: B  207 GLN cc_start: 0.8268 (mm110) cc_final: 0.7988 (mm110)
REVERT: B  213 ARG cc_start: 0.8179 (mtt180) cc_final: 0.7882 (mtt180)
REVERT: B  236 LEU cc_start: 0.8889 (tt) cc_final: 0.8619 (tt)
REVERT: B  237 LYS cc_start: 0.8887 (ttmt) cc_final: 0.8674 (tttt)
REVERT: B  240 LEU cc_start: 0.8838 (mm) cc_final: 0.8537 (mp)
REVERT: B  244 THR cc_start: 0.8437 (p) cc_final: 0.8053 (t)
REVERT: B  260 ILE cc_start: 0.8647 (tt) cc_final: 0.8393 (pt)
REVERT: B  286 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8408 (mtmm)
REVERT: B  287 GLU cc_start: 0.8141 (tp30) cc_final: 0.7114 (tp30)
REVERT: B  329 LYS cc_start: 0.8403 (pttt) cc_final: 0.8158 (pttt)
REVERT: B  373 THR cc_start: 0.8346 (m) cc_final: 0.8064 (t)
REVERT: B  378 VAL cc_start: 0.8570 (t) cc_final: 0.8292 (p)
REVERT: B  382 ASN cc_start: 0.8520 (m-40) cc_final: 0.8113 (t0)
REVERT: B  391 SER cc_start: 0.8751 (m) cc_final: 0.8324 (p)
REVERT: B  394 PHE cc_start: 0.8504 (t80) cc_final: 0.7489 (t80)
REVERT: B  398 PHE cc_start: 0.7979 (m-80) cc_final: 0.7598 (m-80)
REVERT: B  432 MET cc_start: 0.7970 (tpt) cc_final: 0.7592 (tpt)
REVERT: B  447 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8451 (mtpt)
REVERT: B  473 LYS cc_start: 0.8596 (mtpt) cc_final: 0.8375 (mtpt)
REVERT: B  478 ASP cc_start: 0.7806 (m-30) cc_final: 0.7438 (m-30)
REVERT: B  531 LYS cc_start: 0.8469 (mmmt) cc_final: 0.8250 (mmmm)
REVERT: B  563 LYS cc_start: 0.8832 (mmmt) cc_final: 0.8564 (mmmm)
REVERT: B  681 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8268 (ttmm)
REVERT: B  702 LYS cc_start: 0.7917 (tptp) cc_final: 0.7277 (tttm)
REVERT: B  714 ARG cc_start: 0.8500 (mtm-85) cc_final: 0.8120 (mtm-85)
  outliers start: 55
  outliers final: 40
  residues processed: 363
  average time/residue: 0.3207
  time to fit residues: 156.1026
Evaluate side-chains
  362 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 317
  time to evaluate  : 1.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  543 GLU
Chi-restraints excluded: chain A residue  580 LYS
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  656 HIS
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  677 ARG
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  245 LYS
Chi-restraints excluded: chain B residue  246 ASN
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  255 TYR
Chi-restraints excluded: chain B residue  259 GLU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  540 GLU
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  681 LYS
Chi-restraints excluded: chain B residue  697 ASP
Chi-restraints excluded: chain B residue  700 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 54 optimal weight:    0.0270
   chunk 68 optimal weight:    4.9990
   chunk 111 optimal weight:    0.9990
   chunk 113 optimal weight:    0.0980
   chunk 117 optimal weight:    0.7980
   chunk 95 optimal weight:    0.9980
   chunk 85 optimal weight:    0.0070
   chunk 11 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 99 optimal weight:    0.7980
   chunk 112 optimal weight:    0.8980
   overall best weight:    0.3456

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
A 382 ASN
A 457 ASN
A 656 HIS
B  34 GLN
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.121493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.102251 restraints weight = 18196.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.93
r_work: 0.3226 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.3963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10406  Z= 0.136
  Angle     :  0.633   9.626  14142  Z= 0.319
  Chirality :  0.043   0.178   1718
  Planarity :  0.004   0.048   1760
  Dihedral  :  5.594  82.821   1431
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 23.17 %
    Favored  : 71.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.24), residues: 1322
  helix:  0.54 (0.18), residues: 852
  sheet: -1.86 (0.95), residues: 36
  loop : -2.13 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 472 
 HIS   0.017   0.001   HIS A 656 
 PHE   0.016   0.001   PHE A 394 
 TYR   0.013   0.001   TYR B 247 
 ARG   0.012   0.001   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03874 (  562)
  hydrogen bonds       : angle       3.89733 ( 1650)
  covalent geometry    : bond        0.00307 (10406)
  covalent geometry    : angle       0.63337 (14142)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  380 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 322
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8503 (t)
REVERT: A   36 ARG cc_start: 0.8125 (tpp-160) cc_final: 0.7614 (mpp-170)
REVERT: A   38 ARG cc_start: 0.8097 (ttm110) cc_final: 0.7862 (ttp-110)
REVERT: A   48 ASP cc_start: 0.8253 (t70) cc_final: 0.7887 (p0)
REVERT: A   87 ASP cc_start: 0.7323 (m-30) cc_final: 0.6933 (t0)
REVERT: A   94 THR cc_start: 0.8502 (t) cc_final: 0.8183 (p)
REVERT: A  195 LEU cc_start: 0.8586 (tp) cc_final: 0.8307 (tp)
REVERT: A  236 LEU cc_start: 0.8768 (tp) cc_final: 0.8426 (tt)
REVERT: A  245 LYS cc_start: 0.8317 (ttmm) cc_final: 0.7927 (ttmm)
REVERT: A  247 TYR cc_start: 0.8191 (m-10) cc_final: 0.7580 (m-10)
REVERT: A  251 LEU cc_start: 0.8667 (mm) cc_final: 0.8278 (mm)
REVERT: A  254 ILE cc_start: 0.8462 (pt) cc_final: 0.8204 (pt)
REVERT: A  276 LEU cc_start: 0.8602 (tp) cc_final: 0.8335 (tp)
REVERT: A  369 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7928 (mmtt)
REVERT: A  384 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7294 (mm-30)
REVERT: A  385 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7741 (t80)
REVERT: A  391 SER cc_start: 0.8754 (m) cc_final: 0.8391 (p)
REVERT: A  394 PHE cc_start: 0.8575 (t80) cc_final: 0.8157 (t80)
REVERT: A  398 PHE cc_start: 0.8109 (m-80) cc_final: 0.7672 (m-10)
REVERT: A  414 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7468 (tm-30)
REVERT: A  432 MET cc_start: 0.7740 (tpt) cc_final: 0.7376 (tpt)
REVERT: A  447 LYS cc_start: 0.8839 (mtpt) cc_final: 0.8425 (mtpt)
REVERT: A  470 ARG cc_start: 0.7986 (tpp80) cc_final: 0.7755 (tpp80)
REVERT: A  475 ASN cc_start: 0.7368 (m-40) cc_final: 0.6988 (m-40)
REVERT: A  478 ASP cc_start: 0.7507 (m-30) cc_final: 0.7165 (m-30)
REVERT: A  563 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8437 (mmmt)
REVERT: A  573 ASP cc_start: 0.7847 (t0) cc_final: 0.7528 (t0)
REVERT: A  581 ARG cc_start: 0.8008 (mmt180) cc_final: 0.7642 (mtp85)
REVERT: A  677 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8021 (ttt-90)
REVERT: A  698 ASP cc_start: 0.7678 (t0) cc_final: 0.7302 (t0)
REVERT: B   66 LYS cc_start: 0.8096 (tppt) cc_final: 0.7834 (tppt)
REVERT: B   71 ILE cc_start: 0.8636 (tt) cc_final: 0.8277 (tp)
REVERT: B  155 MET cc_start: 0.8263 (mpp) cc_final: 0.7952 (mpp)
REVERT: B  195 LEU cc_start: 0.8599 (tp) cc_final: 0.8254 (tp)
REVERT: B  213 ARG cc_start: 0.8172 (mtt180) cc_final: 0.7893 (mtt180)
REVERT: B  236 LEU cc_start: 0.8879 (tt) cc_final: 0.8598 (tt)
REVERT: B  237 LYS cc_start: 0.8902 (ttmt) cc_final: 0.8653 (tttt)
REVERT: B  240 LEU cc_start: 0.8850 (mm) cc_final: 0.8583 (mp)
REVERT: B  244 THR cc_start: 0.8442 (p) cc_final: 0.7854 (t)
REVERT: B  260 ILE cc_start: 0.8654 (tt) cc_final: 0.8415 (pt)
REVERT: B  286 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8393 (mtmm)
REVERT: B  287 GLU cc_start: 0.8148 (tp30) cc_final: 0.7143 (tp30)
REVERT: B  329 LYS cc_start: 0.8394 (pttt) cc_final: 0.8181 (pttt)
REVERT: B  373 THR cc_start: 0.8328 (m) cc_final: 0.8048 (t)
REVERT: B  378 VAL cc_start: 0.8561 (t) cc_final: 0.8274 (p)
REVERT: B  380 ASP cc_start: 0.8230 (t0) cc_final: 0.8025 (t0)
REVERT: B  391 SER cc_start: 0.8759 (m) cc_final: 0.8314 (p)
REVERT: B  394 PHE cc_start: 0.8502 (t80) cc_final: 0.7603 (t80)
REVERT: B  398 PHE cc_start: 0.7976 (m-80) cc_final: 0.7609 (m-10)
REVERT: B  432 MET cc_start: 0.7950 (tpt) cc_final: 0.7572 (tpt)
REVERT: B  447 LYS cc_start: 0.8854 (mtpt) cc_final: 0.8443 (mtpt)
REVERT: B  459 LYS cc_start: 0.8767 (ttpp) cc_final: 0.8550 (ttpp)
REVERT: B  473 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8400 (mtpt)
REVERT: B  478 ASP cc_start: 0.7864 (m-30) cc_final: 0.7448 (m-30)
REVERT: B  531 LYS cc_start: 0.8470 (mmmt) cc_final: 0.8175 (mmmm)
REVERT: B  563 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8578 (mmmm)
REVERT: B  573 ASP cc_start: 0.7157 (t70) cc_final: 0.6482 (p0)
REVERT: B  677 ARG cc_start: 0.8594 (tpt-90) cc_final: 0.8080 (tpt-90)
REVERT: B  681 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8210 (ttmm)
REVERT: B  702 LYS cc_start: 0.7626 (tptp) cc_final: 0.7232 (tptm)
REVERT: B  714 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.8109 (mtm-85)
  outliers start: 58
  outliers final: 41
  residues processed: 359
  average time/residue: 0.2728
  time to fit residues: 129.9524
Evaluate side-chains
  360 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 315
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  229 PHE
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  457 ASN
Chi-restraints excluded: chain A residue  541 GLU
Chi-restraints excluded: chain A residue  543 GLU
Chi-restraints excluded: chain A residue  580 LYS
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  677 ARG
Chi-restraints excluded: chain A residue  682 GLU
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  245 LYS
Chi-restraints excluded: chain B residue  246 ASN
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  255 TYR
Chi-restraints excluded: chain B residue  259 GLU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  681 LYS
Chi-restraints excluded: chain B residue  697 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 131 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 114 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 382 ASN
A 656 HIS
A 728 HIS
B  34 GLN
B 135 HIS
B 382 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.118523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.099552 restraints weight = 18115.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 2.88
r_work: 0.3180 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.4144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.089  10406  Z= 0.210
  Angle     :  0.676   9.857  14142  Z= 0.346
  Chirality :  0.046   0.199   1718
  Planarity :  0.004   0.049   1760
  Dihedral  :  5.670  81.706   1431
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 23.98 %
    Favored  : 71.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.24), residues: 1322
  helix:  0.41 (0.18), residues: 868
  sheet: -1.68 (0.95), residues: 36
  loop : -2.17 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  74 
 HIS   0.010   0.001   HIS A 656 
 PHE   0.014   0.001   PHE A 394 
 TYR   0.016   0.002   TYR B  20 
 ARG   0.010   0.001   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04196 (  562)
  hydrogen bonds       : angle       3.93970 ( 1650)
  covalent geometry    : bond        0.00466 (10406)
  covalent geometry    : angle       0.67587 (14142)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  381 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 325
  time to evaluate  : 1.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8583 (t)
REVERT: A   36 ARG cc_start: 0.8172 (tpp-160) cc_final: 0.7641 (mpp-170)
REVERT: A   48 ASP cc_start: 0.8231 (t70) cc_final: 0.7904 (p0)
REVERT: A   87 ASP cc_start: 0.7347 (m-30) cc_final: 0.7043 (t0)
REVERT: A   88 ILE cc_start: 0.7507 (mm) cc_final: 0.7287 (mm)
REVERT: A   94 THR cc_start: 0.8519 (t) cc_final: 0.8137 (p)
REVERT: A  195 LEU cc_start: 0.8598 (tp) cc_final: 0.8333 (tp)
REVERT: A  236 LEU cc_start: 0.8792 (tp) cc_final: 0.8383 (tt)
REVERT: A  245 LYS cc_start: 0.8358 (ttmm) cc_final: 0.7950 (ttmm)
REVERT: A  247 TYR cc_start: 0.8192 (m-10) cc_final: 0.7549 (m-10)
REVERT: A  276 LEU cc_start: 0.8672 (tp) cc_final: 0.8407 (tp)
REVERT: A  277 LEU cc_start: 0.8637 (tp) cc_final: 0.8405 (tp)
REVERT: A  378 VAL cc_start: 0.8089 (OUTLIER) cc_final: 0.7769 (p)
REVERT: A  384 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7373 (mm-30)
REVERT: A  391 SER cc_start: 0.8766 (m) cc_final: 0.8401 (p)
REVERT: A  414 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7491 (tm-30)
REVERT: A  432 MET cc_start: 0.7855 (tpt) cc_final: 0.7465 (tpt)
REVERT: A  447 LYS cc_start: 0.8882 (mtpt) cc_final: 0.8453 (mtpt)
REVERT: A  470 ARG cc_start: 0.8048 (tpp80) cc_final: 0.7814 (tpp80)
REVERT: A  475 ASN cc_start: 0.7533 (m-40) cc_final: 0.7059 (m-40)
REVERT: A  478 ASP cc_start: 0.7589 (m-30) cc_final: 0.7326 (m-30)
REVERT: A  563 LYS cc_start: 0.8848 (mmmt) cc_final: 0.8391 (mmmt)
REVERT: A  573 ASP cc_start: 0.7976 (t0) cc_final: 0.7630 (t0)
REVERT: A  587 ARG cc_start: 0.7407 (mmm-85) cc_final: 0.6949 (tpt170)
REVERT: A  677 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8041 (ttt-90)
REVERT: A  698 ASP cc_start: 0.7701 (t0) cc_final: 0.7309 (t0)
REVERT: B   66 LYS cc_start: 0.8174 (tppt) cc_final: 0.7887 (tppt)
REVERT: B   71 ILE cc_start: 0.8693 (tt) cc_final: 0.8339 (tp)
REVERT: B  155 MET cc_start: 0.8288 (mpp) cc_final: 0.7954 (mpp)
REVERT: B  195 LEU cc_start: 0.8643 (tp) cc_final: 0.8297 (tp)
REVERT: B  213 ARG cc_start: 0.8196 (mtt180) cc_final: 0.7987 (ttp-170)
REVERT: B  217 ASP cc_start: 0.7738 (t0) cc_final: 0.7529 (t0)
REVERT: B  236 LEU cc_start: 0.8873 (tt) cc_final: 0.8581 (tt)
REVERT: B  240 LEU cc_start: 0.8863 (mm) cc_final: 0.8622 (mp)
REVERT: B  244 THR cc_start: 0.8493 (p) cc_final: 0.8282 (t)
REVERT: B  260 ILE cc_start: 0.8660 (tt) cc_final: 0.8408 (pt)
REVERT: B  286 LYS cc_start: 0.8763 (ttmm) cc_final: 0.8403 (mtmm)
REVERT: B  287 GLU cc_start: 0.8199 (tp30) cc_final: 0.7226 (tp30)
REVERT: B  378 VAL cc_start: 0.8548 (t) cc_final: 0.8293 (p)
REVERT: B  380 ASP cc_start: 0.8218 (t0) cc_final: 0.7987 (t0)
REVERT: B  382 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8276 (t0)
REVERT: B  391 SER cc_start: 0.8807 (m) cc_final: 0.8335 (p)
REVERT: B  398 PHE cc_start: 0.7999 (m-80) cc_final: 0.7662 (m-80)
REVERT: B  432 MET cc_start: 0.7971 (tpt) cc_final: 0.7597 (tpt)
REVERT: B  447 LYS cc_start: 0.8851 (mtpt) cc_final: 0.8469 (mtpt)
REVERT: B  459 LYS cc_start: 0.8808 (ttpp) cc_final: 0.8568 (ttpp)
REVERT: B  473 LYS cc_start: 0.8626 (mtpt) cc_final: 0.8426 (mtpt)
REVERT: B  563 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8536 (mmmt)
REVERT: B  573 ASP cc_start: 0.7230 (t70) cc_final: 0.6529 (p0)
REVERT: B  677 ARG cc_start: 0.8584 (tpt-90) cc_final: 0.8047 (tpt-90)
REVERT: B  681 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8202 (ttmm)
REVERT: B  702 LYS cc_start: 0.7795 (tptp) cc_final: 0.7300 (tttm)
REVERT: B  714 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.8135 (mtm-85)
  outliers start: 56
  outliers final: 40
  residues processed: 360
  average time/residue: 0.2883
  time to fit residues: 138.7269
Evaluate side-chains
  367 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 322
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  382 ASN
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  543 GLU
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  677 ARG
Chi-restraints excluded: chain A residue  682 GLU
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  103 MET
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  245 LYS
Chi-restraints excluded: chain B residue  246 ASN
Chi-restraints excluded: chain B residue  255 TYR
Chi-restraints excluded: chain B residue  259 GLU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  382 ASN
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  681 LYS
Chi-restraints excluded: chain B residue  697 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0980
   chunk 77 optimal weight:    1.9990
   chunk 110 optimal weight:    0.7980
   chunk 112 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 160 HIS
A 457 ASN
A 656 HIS
B  34 GLN
B 382 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.119519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.100471 restraints weight = 18106.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 2.88
r_work: 0.3196 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.4273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  10406  Z= 0.168
  Angle     :  0.676   9.878  14142  Z= 0.344
  Chirality :  0.045   0.192   1718
  Planarity :  0.004   0.047   1760
  Dihedral  :  5.701  82.689   1431
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 25.22 %
    Favored  : 69.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.24), residues: 1322
  helix:  0.46 (0.18), residues: 868
  sheet: -1.57 (0.97), residues: 36
  loop : -2.12 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 472 
 HIS   0.011   0.001   HIS A 160 
 PHE   0.023   0.001   PHE A 394 
 TYR   0.012   0.001   TYR B  20 
 ARG   0.014   0.001   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04086 (  562)
  hydrogen bonds       : angle       3.92445 ( 1650)
  covalent geometry    : bond        0.00379 (10406)
  covalent geometry    : angle       0.67593 (14142)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  372 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 317
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8563 (t)
REVERT: A   36 ARG cc_start: 0.8153 (tpp-160) cc_final: 0.7623 (mpp-170)
REVERT: A   48 ASP cc_start: 0.8249 (t70) cc_final: 0.7875 (p0)
REVERT: A   87 ASP cc_start: 0.7384 (m-30) cc_final: 0.7067 (t0)
REVERT: A   88 ILE cc_start: 0.7532 (mm) cc_final: 0.7309 (mm)
REVERT: A   94 THR cc_start: 0.8531 (t) cc_final: 0.8201 (p)
REVERT: A  195 LEU cc_start: 0.8571 (tp) cc_final: 0.8303 (tp)
REVERT: A  236 LEU cc_start: 0.8788 (tp) cc_final: 0.8434 (tt)
REVERT: A  245 LYS cc_start: 0.8321 (ttmm) cc_final: 0.7926 (ttmm)
REVERT: A  247 TYR cc_start: 0.8157 (m-10) cc_final: 0.7517 (m-10)
REVERT: A  276 LEU cc_start: 0.8667 (tp) cc_final: 0.8410 (tp)
REVERT: A  277 LEU cc_start: 0.8625 (tp) cc_final: 0.8390 (tp)
REVERT: A  378 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7664 (p)
REVERT: A  391 SER cc_start: 0.8773 (m) cc_final: 0.8413 (p)
REVERT: A  394 PHE cc_start: 0.8621 (t80) cc_final: 0.8325 (t80)
REVERT: A  398 PHE cc_start: 0.8129 (m-80) cc_final: 0.7802 (m-10)
REVERT: A  414 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7470 (tm-30)
REVERT: A  432 MET cc_start: 0.7826 (tpt) cc_final: 0.7437 (tpt)
REVERT: A  447 LYS cc_start: 0.8857 (mtpt) cc_final: 0.8457 (mtpt)
REVERT: A  470 ARG cc_start: 0.7991 (tpp80) cc_final: 0.7769 (tpp80)
REVERT: A  475 ASN cc_start: 0.7414 (m-40) cc_final: 0.6894 (m-40)
REVERT: A  478 ASP cc_start: 0.7572 (m-30) cc_final: 0.7298 (m-30)
REVERT: A  560 ASP cc_start: 0.8270 (m-30) cc_final: 0.7844 (m-30)
REVERT: A  563 LYS cc_start: 0.8833 (mmmt) cc_final: 0.8425 (mmmt)
REVERT: A  573 ASP cc_start: 0.7954 (t0) cc_final: 0.7624 (t0)
REVERT: A  587 ARG cc_start: 0.7411 (mmm-85) cc_final: 0.6972 (tpt170)
REVERT: A  677 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7578 (ttt-90)
REVERT: A  681 LYS cc_start: 0.8333 (tptt) cc_final: 0.7956 (mptt)
REVERT: A  698 ASP cc_start: 0.7654 (t0) cc_final: 0.7280 (t0)
REVERT: B   38 ARG cc_start: 0.8432 (mtp-110) cc_final: 0.8230 (ttm110)
REVERT: B   66 LYS cc_start: 0.8122 (tppt) cc_final: 0.7858 (tppt)
REVERT: B   71 ILE cc_start: 0.8612 (tt) cc_final: 0.8264 (tp)
REVERT: B  155 MET cc_start: 0.8263 (mpp) cc_final: 0.7940 (mpp)
REVERT: B  195 LEU cc_start: 0.8630 (tp) cc_final: 0.8292 (tp)
REVERT: B  213 ARG cc_start: 0.8163 (mtt180) cc_final: 0.7928 (ttm170)
REVERT: B  236 LEU cc_start: 0.8868 (tt) cc_final: 0.8548 (tt)
REVERT: B  260 ILE cc_start: 0.8649 (tt) cc_final: 0.8395 (pt)
REVERT: B  286 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8467 (mtmm)
REVERT: B  287 GLU cc_start: 0.8189 (tp30) cc_final: 0.7213 (tp30)
REVERT: B  373 THR cc_start: 0.8291 (m) cc_final: 0.8043 (t)
REVERT: B  378 VAL cc_start: 0.8585 (t) cc_final: 0.8327 (p)
REVERT: B  380 ASP cc_start: 0.8292 (t0) cc_final: 0.8054 (t0)
REVERT: B  382 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8243 (t0)
REVERT: B  391 SER cc_start: 0.8804 (m) cc_final: 0.8354 (p)
REVERT: B  398 PHE cc_start: 0.7969 (m-80) cc_final: 0.7638 (m-80)
REVERT: B  432 MET cc_start: 0.7918 (tpt) cc_final: 0.7533 (tpt)
REVERT: B  447 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8460 (mtpt)
REVERT: B  459 LYS cc_start: 0.8798 (ttpp) cc_final: 0.8552 (ttpp)
REVERT: B  478 ASP cc_start: 0.7676 (m-30) cc_final: 0.7373 (m-30)
REVERT: B  554 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7820 (mt)
REVERT: B  573 ASP cc_start: 0.7186 (t70) cc_final: 0.6641 (p0)
REVERT: B  674 ARG cc_start: 0.7978 (mtt180) cc_final: 0.7715 (mtm-85)
REVERT: B  681 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8224 (ttmm)
REVERT: B  702 LYS cc_start: 0.7665 (tptp) cc_final: 0.7289 (tptp)
  outliers start: 55
  outliers final: 39
  residues processed: 351
  average time/residue: 0.2772
  time to fit residues: 131.4101
Evaluate side-chains
  369 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 324
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  229 PHE
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  457 ASN
Chi-restraints excluded: chain A residue  543 GLU
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  656 HIS
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  677 ARG
Chi-restraints excluded: chain A residue  682 GLU
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  103 MET
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  246 ASN
Chi-restraints excluded: chain B residue  259 GLU
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  382 ASN
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  554 ILE
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  681 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 16 optimal weight:    0.4980
   chunk 20 optimal weight:    0.4980
   chunk 26 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 104 optimal weight:    0.0670
   chunk 37 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 110 optimal weight:    1.9990
   chunk 102 optimal weight:    0.6980
   chunk 76 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
A 160 HIS
A 382 ASN
A 656 HIS
B  34 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.119708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.100669 restraints weight = 18009.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 2.90
r_work: 0.3204 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.4321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  10406  Z= 0.161
  Angle     :  0.685   9.637  14142  Z= 0.346
  Chirality :  0.045   0.195   1718
  Planarity :  0.004   0.047   1760
  Dihedral  :  5.579  82.692   1429
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 26.56 %
    Favored  : 69.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.24), residues: 1322
  helix:  0.49 (0.18), residues: 868
  sheet: -1.45 (1.00), residues: 36
  loop : -2.10 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 472 
 HIS   0.016   0.001   HIS A 656 
 PHE   0.019   0.001   PHE A 394 
 TYR   0.012   0.001   TYR B  20 
 ARG   0.014   0.001   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03995 (  562)
  hydrogen bonds       : angle       3.89777 ( 1650)
  covalent geometry    : bond        0.00365 (10406)
  covalent geometry    : angle       0.68511 (14142)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  377 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 329
  time to evaluate  : 1.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8526 (t)
REVERT: A   36 ARG cc_start: 0.8163 (tpp-160) cc_final: 0.7602 (mpp-170)
REVERT: A   48 ASP cc_start: 0.8225 (t70) cc_final: 0.7873 (p0)
REVERT: A   87 ASP cc_start: 0.7380 (m-30) cc_final: 0.7079 (t0)
REVERT: A   88 ILE cc_start: 0.7525 (mm) cc_final: 0.7313 (mm)
REVERT: A   94 THR cc_start: 0.8503 (t) cc_final: 0.8108 (p)
REVERT: A  195 LEU cc_start: 0.8553 (tp) cc_final: 0.8291 (tp)
REVERT: A  236 LEU cc_start: 0.8778 (tp) cc_final: 0.8423 (tt)
REVERT: A  245 LYS cc_start: 0.8325 (ttmm) cc_final: 0.7926 (ttmm)
REVERT: A  247 TYR cc_start: 0.8138 (m-10) cc_final: 0.7521 (m-10)
REVERT: A  276 LEU cc_start: 0.8667 (tp) cc_final: 0.8406 (tp)
REVERT: A  277 LEU cc_start: 0.8610 (tp) cc_final: 0.8375 (tp)
REVERT: A  385 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8239 (m-80)
REVERT: A  391 SER cc_start: 0.8766 (m) cc_final: 0.8397 (p)
REVERT: A  414 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7464 (tm-30)
REVERT: A  432 MET cc_start: 0.7814 (tpt) cc_final: 0.7423 (tpt)
REVERT: A  447 LYS cc_start: 0.8871 (mtpt) cc_final: 0.8599 (mtpt)
REVERT: A  470 ARG cc_start: 0.8003 (tpp80) cc_final: 0.7776 (tpp80)
REVERT: A  475 ASN cc_start: 0.7413 (m-40) cc_final: 0.6897 (m-40)
REVERT: A  478 ASP cc_start: 0.7563 (m-30) cc_final: 0.7299 (m-30)
REVERT: A  560 ASP cc_start: 0.8283 (m-30) cc_final: 0.7536 (m-30)
REVERT: A  563 LYS cc_start: 0.8838 (mmmt) cc_final: 0.8422 (mmmt)
REVERT: A  573 ASP cc_start: 0.7925 (t0) cc_final: 0.7611 (t0)
REVERT: A  587 ARG cc_start: 0.7406 (mmm-85) cc_final: 0.6966 (tpt170)
REVERT: A  677 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7594 (ttt-90)
REVERT: A  681 LYS cc_start: 0.8330 (tptt) cc_final: 0.7957 (mptt)
REVERT: A  698 ASP cc_start: 0.7615 (t0) cc_final: 0.7283 (t0)
REVERT: B   66 LYS cc_start: 0.8124 (tppt) cc_final: 0.7872 (tppt)
REVERT: B   71 ILE cc_start: 0.8610 (tt) cc_final: 0.8269 (tp)
REVERT: B  155 MET cc_start: 0.8247 (mpp) cc_final: 0.7930 (mpp)
REVERT: B  195 LEU cc_start: 0.8618 (tp) cc_final: 0.8277 (tp)
REVERT: B  213 ARG cc_start: 0.8159 (mtt180) cc_final: 0.7910 (mtt180)
REVERT: B  236 LEU cc_start: 0.8883 (tt) cc_final: 0.8562 (tt)
REVERT: B  240 LEU cc_start: 0.8873 (mm) cc_final: 0.8528 (mp)
REVERT: B  260 ILE cc_start: 0.8633 (tt) cc_final: 0.8420 (pt)
REVERT: B  286 LYS cc_start: 0.8768 (ttmm) cc_final: 0.8457 (mtmm)
REVERT: B  287 GLU cc_start: 0.8170 (tp30) cc_final: 0.7195 (tp30)
REVERT: B  318 ASN cc_start: 0.8495 (t0) cc_final: 0.8249 (t0)
REVERT: B  324 ASN cc_start: 0.8573 (t0) cc_final: 0.8187 (t0)
REVERT: B  373 THR cc_start: 0.8279 (m) cc_final: 0.8041 (t)
REVERT: B  378 VAL cc_start: 0.8582 (t) cc_final: 0.8328 (p)
REVERT: B  380 ASP cc_start: 0.8216 (t0) cc_final: 0.7943 (t0)
REVERT: B  391 SER cc_start: 0.8812 (m) cc_final: 0.8363 (p)
REVERT: B  398 PHE cc_start: 0.7931 (m-80) cc_final: 0.7625 (m-10)
REVERT: B  432 MET cc_start: 0.7886 (tpt) cc_final: 0.7493 (tpt)
REVERT: B  447 LYS cc_start: 0.8830 (mtpt) cc_final: 0.8436 (mtpt)
REVERT: B  459 LYS cc_start: 0.8784 (ttpp) cc_final: 0.8530 (ttpp)
REVERT: B  478 ASP cc_start: 0.7620 (m-30) cc_final: 0.7277 (m-30)
REVERT: B  554 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7829 (mt)
REVERT: B  573 ASP cc_start: 0.7188 (t70) cc_final: 0.6509 (p0)
REVERT: B  681 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8221 (ttmm)
REVERT: B  702 LYS cc_start: 0.7643 (tptp) cc_final: 0.7224 (tttm)
  outliers start: 48
  outliers final: 38
  residues processed: 360
  average time/residue: 0.2680
  time to fit residues: 127.2431
Evaluate side-chains
  370 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 327
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  229 PHE
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  543 GLU
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  656 HIS
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  677 ARG
Chi-restraints excluded: chain A residue  682 GLU
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  246 ASN
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  554 ILE
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  681 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 44 optimal weight:    0.1980
   chunk 4 optimal weight:    3.9990
   chunk 86 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    0.1980
   chunk 52 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 87 optimal weight:    0.5980
   chunk 119 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 160 HIS
A 656 HIS
** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 567 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.119885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.100933 restraints weight = 17932.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 2.88
r_work: 0.3209 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.4376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  10406  Z= 0.160
  Angle     :  0.686  10.439  14142  Z= 0.344
  Chirality :  0.044   0.194   1718
  Planarity :  0.004   0.045   1760
  Dihedral  :  5.578  82.864   1429
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 26.38 %
    Favored  : 69.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.24), residues: 1322
  helix:  0.59 (0.18), residues: 860
  sheet: -1.56 (0.99), residues: 36
  loop : -2.00 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 472 
 HIS   0.014   0.001   HIS A 656 
 PHE   0.014   0.001   PHE A 385 
 TYR   0.012   0.001   TYR B  20 
 ARG   0.013   0.001   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03981 (  562)
  hydrogen bonds       : angle       3.88831 ( 1650)
  covalent geometry    : bond        0.00365 (10406)
  covalent geometry    : angle       0.68603 (14142)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5115.56 seconds
wall clock time: 90 minutes 32.90 seconds (5432.90 seconds total)