Starting phenix.real_space_refine
on Wed Mar  4 02:35:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wk1_32555/03_2026/7wk1_32555.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wk1_32555/03_2026/7wk1_32555.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wk1_32555/03_2026/7wk1_32555.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wk1_32555/03_2026/7wk1_32555.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wk1_32555/03_2026/7wk1_32555.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wk1_32555/03_2026/7wk1_32555.map"
  }
  resolution = 3.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     Cl      2      4.86       5
     C    6656      2.51       5
     N    1684      2.21       5
     O    1816      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10200
  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: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.38, per 1000 atoms: 0.23
  Number of scatterers: 10200
  At special positions: 0
  Unit cell: (86.818, 126.566, 117.152, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S      42     16.00
     O    1816      8.00
     N    1684      7.00
     C    6656      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: 0.82
  Conformation dependent library (CDL) restraints added in 421.4 milliseconds
  

  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 7 sheets defined
      66.8% alpha, 3.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 34
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.602A  pdb=" N   CYS A  54 " --> pdb=" O   LEU A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 69
      removed outlier: 3.882A  pdb=" N   ALA A  61 " --> pdb=" O   SER A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 75
      removed outlier: 4.054A  pdb=" N   TRP A  74 " --> pdb=" O   PRO A  70 " (cutoff:3.500A)
      removed outlier: 3.535A  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: 4.909A  pdb=" N   LEU A  85 " --> pdb=" O   LYS A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 120
      removed outlier: 3.851A  pdb=" N   GLY A 116 " --> pdb=" O   PRO A 112 " (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: 3.804A  pdb=" N   HIS A 160 " --> pdb=" O   PRO A 157 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   PHE A 161 " --> pdb=" O   ASP A 158 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 157 through 161'
    Processing helix  chain 'A' and resid 179 through 206
      removed outlier: 3.883A  pdb=" N   ALA A 183 " --> pdb=" O   GLY A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 215
      removed outlier: 3.563A  pdb=" N   VAL A 212 " --> pdb=" O   GLY A 209 " (cutoff:3.500A)
      removed outlier: 3.865A  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: 3.621A  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: 3.758A  pdb=" N   GLU A 384 " --> pdb=" O   ASP A 380 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE A 397 " --> pdb=" O   VAL A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 417
      removed outlier: 3.716A  pdb=" N   VAL A 412 " --> pdb=" O   SER A 408 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   GLN A 413 " --> pdb=" O   ARG A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 437
      removed outlier: 3.662A  pdb=" N   VAL A 431 " --> pdb=" O   SER A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 458
      removed outlier: 3.784A  pdb=" N   LEU A 450 " --> pdb=" O   GLN A 446 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   VAL A 453 " --> pdb=" O   VAL A 449 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   VAL A 454 " --> pdb=" O   LEU A 450 " (cutoff:3.500A)
      removed outlier: 3.977A  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
    Processing helix  chain 'A' and resid 475 through 492
      removed outlier: 3.515A  pdb=" N   ALA A 479 " --> pdb=" O   ASN A 475 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE A 490 " --> pdb=" O   CYS A 486 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU A 492 " --> pdb=" O   MET A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 515
      removed outlier: 3.569A  pdb=" N   LEU A 498 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      removed outlier: 3.676A  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: 3.782A  pdb=" N   TYR A 578 " --> pdb=" O   ALA A 574 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ARG A 587 " --> pdb=" O   LYS A 583 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ILE A 588 " --> pdb=" O   ALA A 584 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A 591 " --> pdb=" O   ARG A 587 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ILE A 592 " --> pdb=" O   ILE A 588 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   LYS A 593 " --> pdb=" O   GLN A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 686
      removed outlier: 3.754A  pdb=" N   SER A 675 " --> pdb=" O   VAL A 671 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ILE A 686 " --> pdb=" O   GLU A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 696 through 706
      removed outlier: 3.562A  pdb=" N   GLN A 705 " --> pdb=" O   GLU A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 718
      removed outlier: 3.529A  pdb=" N   ARG A 717 " --> pdb=" O   ARG A 714 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 736
      removed outlier: 3.857A  pdb=" N   ALA A 725 " --> pdb=" O   THR A 721 " (cutoff:3.500A)
      removed outlier: 3.548A  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: 3.552A  pdb=" N   LEU B  50 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ALA B  51 " --> pdb=" O   ARG B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 69
      removed outlier: 3.752A  pdb=" N   ALA B  61 " --> pdb=" O   SER B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 75
      removed outlier: 4.080A  pdb=" N   TRP B  74 " --> pdb=" O   PRO B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 105
      removed outlier: 3.729A  pdb=" N   SER B  86 " --> pdb=" O   GLU B  82 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ILE B  89 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   VAL B  92 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU B 100 " --> pdb=" O   LEU B  96 " (cutoff:3.500A)
      removed outlier: 3.723A  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: 3.978A  pdb=" N   LEU B 117 " --> pdb=" O   VAL B 113 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   TYR B 118 " --> pdb=" O   GLN B 114 " (cutoff:3.500A)
      removed outlier: 3.505A  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: 3.659A  pdb=" N   VAL B 151 " --> pdb=" O   MET B 147 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER B 154 " --> pdb=" O   SER B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 161
      removed outlier: 3.571A  pdb=" N   HIS B 160 " --> pdb=" O   PRO B 157 " (cutoff:3.500A)
      removed outlier: 3.552A  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: 3.981A  pdb=" N   ALA B 184 " --> pdb=" O   THR B 180 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ARG B 185 " --> pdb=" O   ARG B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 215
      removed outlier: 3.590A  pdb=" N   VAL B 212 " --> pdb=" O   GLY B 209 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   TYR B 214 " --> pdb=" O   ILE B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 241
      removed outlier: 3.569A  pdb=" N   PHE B 229 " --> pdb=" O   THR B 225 " (cutoff:3.500A)
      removed outlier: 3.749A  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: 3.641A  pdb=" N   THR B 278 " --> pdb=" O   ALA B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 317
      removed outlier: 3.514A  pdb=" N   ALA B 317 " --> pdb=" O   ILE B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 376
      removed outlier: 3.795A  pdb=" N   SER B 355 " --> pdb=" O   ALA B 351 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   TYR B 361 " --> pdb=" O   ALA B 357 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ALA B 364 " --> pdb=" O   ALA B 360 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LYS B 374 " --> pdb=" O   VAL B 370 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   HIS B 375 " --> pdb=" O   TYR B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 397
      removed outlier: 3.963A  pdb=" N   GLU B 384 " --> pdb=" O   ASP B 380 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   PHE B 385 " --> pdb=" O   GLY B 381 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ILE B 386 " --> pdb=" O   ASN B 382 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   PHE B 397 " --> pdb=" O   VAL B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 416
      removed outlier: 3.740A  pdb=" N   VAL B 412 " --> pdb=" O   SER B 408 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   GLN B 413 " --> pdb=" O   ARG B 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 437
      removed outlier: 3.611A  pdb=" N   VAL B 436 " --> pdb=" O   MET B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 458
      removed outlier: 3.779A  pdb=" N   LEU B 450 " --> pdb=" O   GLN B 446 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   VAL B 454 " --> pdb=" O   LEU B 450 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ILE B 455 " --> pdb=" O   ALA B 451 " (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
    Processing helix  chain 'B' and resid 475 through 492
      removed outlier: 3.550A  pdb=" N   ALA B 479 " --> pdb=" O   ASN B 475 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ILE B 490 " --> pdb=" O   CYS B 486 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU B 492 " --> pdb=" O   MET B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 494 through 515
      removed outlier: 3.544A  pdb=" N   LEU B 498 " --> pdb=" O   LEU B 494 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LEU B 499 " --> pdb=" O   ASP B 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 558 through 571
    Processing helix  chain 'B' and resid 573 through 595
      removed outlier: 3.845A  pdb=" N   TYR B 578 " --> pdb=" O   ALA B 574 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   ARG B 587 " --> pdb=" O   LYS B 583 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ILE B 588 " --> pdb=" O   ALA B 584 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ILE B 592 " --> pdb=" O   ILE B 588 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   LYS B 593 " --> pdb=" O   GLN B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 669 through 685
      removed outlier: 4.733A  pdb=" N   SER B 675 " --> pdb=" O   VAL B 671 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU B 676 " --> pdb=" O   GLY B 672 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 706
      removed outlier: 3.828A  pdb=" N   LYS B 702 " --> pdb=" O   ASP B 698 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLN B 705 " --> pdb=" O   GLU B 701 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 714 through 718
      removed outlier: 3.551A  pdb=" N   ARG B 717 " --> pdb=" O   ARG B 714 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 721 through 736
      removed outlier: 3.803A  pdb=" N   ALA B 725 " --> pdb=" O   THR B 721 " (cutoff:3.500A)
      removed outlier: 3.512A  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: 3.607A  pdb=" N   VAL A  22 " --> pdb=" O   VAL B  22 " (cutoff:3.500A)
      removed outlier: 3.617A  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 522 through 523
    Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 549
      removed outlier: 6.670A  pdb=" N   LYS A 546 " --> pdb=" O   VAL A 659 " (cutoff:3.500A)
      removed outlier: 7.387A  pdb=" N   ASP A 661 " --> pdb=" O   LYS A 546 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   LEU A 548 " --> pdb=" O   ASP A 661 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 138 through 139
    Processing sheet with id=AA6, first strand: chain 'B' and resid 522 through 523
    Processing sheet with id=AA7, first strand: chain 'B' and resid 545 through 549
      removed outlier: 6.675A  pdb=" N   LYS B 546 " --> pdb=" O   VAL B 659 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   ASP B 661 " --> pdb=" O   LYS B 546 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   LEU B 548 " --> pdb=" O   ASP B 661 " (cutoff:3.500A)

    570 hydrogen bonds defined for protein.
    1674 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.56

  Time building geometry restraints manager: 1.13 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3212
        1.34 -     1.46: 2260
        1.46 -     1.58: 4864
        1.58 -     1.69: 0
        1.69 -     1.81: 64
  Bond restraints: 10400
  Sorted by residual:
  bond pdb=" CA  VAL A 163 "
       pdb=" CB  VAL A 163 "
    ideal  model  delta    sigma   weight residual
    1.540  1.527  0.014 1.23e-02 6.61e+03 1.21e+00
  bond pdb=" C   VAL B 653 "
       pdb=" N   PRO B 654 "
    ideal  model  delta    sigma   weight residual
    1.334  1.354 -0.020 2.34e-02 1.83e+03 7.04e-01
  bond pdb=" C   VAL A 653 "
       pdb=" N   PRO A 654 "
    ideal  model  delta    sigma   weight residual
    1.334  1.353 -0.020 2.34e-02 1.83e+03 6.95e-01
  bond pdb=" CA  ASP A 669 "
       pdb=" C   ASP A 669 "
    ideal  model  delta    sigma   weight residual
    1.523  1.533 -0.010 1.34e-02 5.57e+03 5.79e-01
  bond pdb=" C   GLY B 166 "
       pdb=" N   ASN B 167 "
    ideal  model  delta    sigma   weight residual
    1.328  1.338 -0.010 1.30e-02 5.92e+03 5.79e-01
  ... (remaining 10395 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.22: 13817
        1.22 -     2.43: 242
        2.43 -     3.65: 55
        3.65 -     4.87: 14
        4.87 -     6.08: 8
  Bond angle restraints: 14136
  Sorted by residual:
  angle pdb=" C   ASP B 467 "
        pdb=" N   VAL B 468 "
        pdb=" CA  VAL B 468 "
      ideal   model   delta    sigma   weight residual
     120.33  122.69   -2.36 8.00e-01 1.56e+00 8.69e+00
  angle pdb=" C   ASP A 669 "
        pdb=" N   VAL A 670 "
        pdb=" CA  VAL A 670 "
      ideal   model   delta    sigma   weight residual
     121.97  126.24   -4.27 1.80e+00 3.09e-01 5.62e+00
  angle pdb=" N   VAL A  80 "
        pdb=" CA  VAL A  80 "
        pdb=" C   VAL A  80 "
      ideal   model   delta    sigma   weight residual
     109.34  113.75   -4.41 2.08e+00 2.31e-01 4.49e+00
  angle pdb=" C   ARG A  79 "
        pdb=" N   VAL A  80 "
        pdb=" CA  VAL A  80 "
      ideal   model   delta    sigma   weight residual
     121.97  125.66   -3.69 1.80e+00 3.09e-01 4.20e+00
  angle pdb=" C   ASP B 669 "
        pdb=" N   VAL B 670 "
        pdb=" CA  VAL B 670 "
      ideal   model   delta    sigma   weight residual
     121.97  125.56   -3.59 1.80e+00 3.09e-01 3.99e+00
  ... (remaining 14131 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.18: 5999
       17.18 -    34.36: 150
       34.36 -    51.53: 22
       51.53 -    68.71: 6
       68.71 -    85.89: 5
  Dihedral angle restraints: 6182
    sinusoidal: 2346
      harmonic: 3836
  Sorted by residual:
  dihedral pdb=" CA  ASP A 669 "
           pdb=" C   ASP A 669 "
           pdb=" N   VAL A 670 "
           pdb=" CA  VAL A 670 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.27  -15.73     0      5.00e+00 4.00e-02 9.90e+00
  dihedral pdb=" N   LYS A 681 "
           pdb=" CA  LYS A 681 "
           pdb=" CB  LYS A 681 "
           pdb=" CG  LYS A 681 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.99  -58.01     3      1.50e+01 4.44e-03 9.46e+00
  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
     -60.00 -113.85   53.85     3      1.50e+01 4.44e-03 9.24e+00
  ... (remaining 6179 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 985
       0.026 -    0.053: 479
       0.053 -    0.079: 171
       0.079 -    0.105: 65
       0.105 -    0.131: 18
  Chirality restraints: 1718
  Sorted by residual:
  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 4.32e-01
  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 4.08e-01
  chirality pdb=" CA  ILE A 331 "
            pdb=" N   ILE A 331 "
            pdb=" C   ILE A 331 "
            pdb=" CB  ILE A 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.04e-01
  ... (remaining 1715 not shown)

  Planarity restraints: 1758
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 552 "    0.023 5.00e-02 4.00e+02   3.49e-02 1.95e+00
        pdb=" N   PRO B 553 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO B 553 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 553 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 552 "    0.023 5.00e-02 4.00e+02   3.45e-02 1.90e+00
        pdb=" N   PRO A 553 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 553 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 553 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 111 "    0.022 5.00e-02 4.00e+02   3.32e-02 1.76e+00
        pdb=" N   PRO A 112 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 112 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 112 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1755 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1226
        2.75 -     3.29: 10788
        3.29 -     3.82: 16684
        3.82 -     4.36: 19765
        4.36 -     4.90: 33560
  Nonbonded interactions: 82023
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  78 "
            pdb=" OD2 ASP A  87 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OH  TYR A 118 "
            pdb=" O   GLY A 334 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   ASP A 669 "
            pdb=" N   GLY A 672 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" OD1 ASN A 475 "
            pdb=" OG1 THR A 477 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" OD1 ASN B 475 "
            pdb=" OG1 THR B 477 "
     model   vdw
     2.248 3.040
  ... (remaining 82018 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: 0.01
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:             3.000
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.370
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
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   0.025  10400  Z= 0.091
  Angle     :  0.443   6.082  14136  Z= 0.251
  Chirality :  0.037   0.131   1718
  Planarity :  0.003   0.035   1758
  Dihedral  :  8.422  85.889   3710
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.22 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  :  4.72 %
    Favored  : 92.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.01 (0.19), residues: 1322
  helix: -2.20 (0.14), residues: 860
  sheet: -3.22 (0.77), residues: 36
  loop : -3.28 (0.26), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 512 
 TYR   0.008   0.001   TYR A 127 
 PHE   0.009   0.001   PHE B 555 
 TRP   0.004   0.001   TRP A  83 
 HIS   0.002   0.000   HIS A 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00169 (10400)
  covalent geometry    : angle       0.44270 (14136)
  hydrogen bonds       : bond        0.23680 (  570)
  hydrogen bonds       : angle       7.26712 ( 1674)

*********************** 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
  347 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 314
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A   73 ASP cc_start: 0.7646 (t0) cc_final: 0.7313 (m-30)
REVERT: A  119 SER cc_start: 0.8633 (t) cc_final: 0.8415 (p)
REVERT: A  269 ILE cc_start: 0.8302 (pt) cc_final: 0.7931 (pt)
REVERT: A  273 ILE cc_start: 0.8837 (mt) cc_final: 0.8585 (mt)
REVERT: A  345 LEU cc_start: 0.6245 (mt) cc_final: 0.5738 (mt)
REVERT: A  350 LEU cc_start: 0.5830 (OUTLIER) cc_final: 0.5410 (pt)
REVERT: A  369 LYS cc_start: 0.8083 (mmtt) cc_final: 0.7580 (mttm)
REVERT: A  385 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.7073 (t80)
REVERT: A  560 ASP cc_start: 0.7912 (m-30) cc_final: 0.7648 (m-30)
REVERT: A  580 LYS cc_start: 0.8180 (mmtt) cc_final: 0.7786 (mtpt)
REVERT: B   66 LYS cc_start: 0.8607 (tppt) cc_final: 0.8018 (mttm)
REVERT: B   73 ASP cc_start: 0.7799 (t0) cc_final: 0.7562 (t0)
REVERT: B   77 LYS cc_start: 0.7489 (pttm) cc_final: 0.7013 (tptt)
REVERT: B  134 ARG cc_start: 0.7776 (mtt90) cc_final: 0.7362 (mtp180)
REVERT: B  350 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.5900 (tm)
REVERT: B  355 SER cc_start: 0.8950 (m) cc_final: 0.8617 (t)
REVERT: B  366 SER cc_start: 0.8939 (t) cc_final: 0.8232 (m)
REVERT: B  560 ASP cc_start: 0.7781 (m-30) cc_final: 0.7536 (m-30)
REVERT: B  580 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7937 (mtpt)
  outliers start: 33
  outliers final: 6
  residues processed: 336
  average time/residue: 0.0981
  time to fit residues: 45.9668
Evaluate side-chains
  184 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 175
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  668 LEU
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  496 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.2980
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 160 HIS
A 230 GLN
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 421 GLN
A 656 HIS
A 728 HIS
A 730 GLN
B 135 HIS
B 160 HIS
B 421 GLN
B 656 HIS
B 728 HIS
B 730 GLN
B 731 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.152367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.118710 restraints weight = 14317.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 2.23
r_work: 0.3289 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10400  Z= 0.178
  Angle     :  0.606   6.012  14136  Z= 0.319
  Chirality :  0.044   0.202   1718
  Planarity :  0.005   0.053   1758
  Dihedral  :  4.803  55.835   1431
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 11.59 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.90 (0.22), residues: 1322
  helix: -0.32 (0.17), residues: 856
  sheet: -3.55 (0.63), residues: 50
  loop : -2.84 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  39 
 TYR   0.025   0.001   TYR A 371 
 PHE   0.022   0.002   PHE A 130 
 TRP   0.008   0.001   TRP B 518 
 HIS   0.009   0.002   HIS A 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (10400)
  covalent geometry    : angle       0.60641 (14136)
  hydrogen bonds       : bond        0.04536 (  570)
  hydrogen bonds       : angle       4.36285 ( 1674)

*********************** 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
  230 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 185
  time to evaluate  : 0.392 
Fit side-chains
REVERT: A   73 ASP cc_start: 0.7832 (t0) cc_final: 0.7372 (t0)
REVERT: A   78 TYR cc_start: 0.6408 (t80) cc_final: 0.6183 (t80)
REVERT: A  119 SER cc_start: 0.9065 (t) cc_final: 0.8748 (p)
REVERT: A  269 ILE cc_start: 0.8343 (pt) cc_final: 0.7959 (pt)
REVERT: A  273 ILE cc_start: 0.8965 (mt) cc_final: 0.8723 (mt)
REVERT: A  306 VAL cc_start: 0.8950 (p) cc_final: 0.8741 (p)
REVERT: A  345 LEU cc_start: 0.6628 (mt) cc_final: 0.6203 (mt)
REVERT: A  350 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5443 (pt)
REVERT: A  369 LYS cc_start: 0.7905 (mmtt) cc_final: 0.7657 (mmtp)
REVERT: A  385 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7475 (t80)
REVERT: A  386 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8646 (pt)
REVERT: A  398 PHE cc_start: 0.7563 (m-80) cc_final: 0.7351 (m-80)
REVERT: A  560 ASP cc_start: 0.8462 (m-30) cc_final: 0.8245 (m-30)
REVERT: A  580 LYS cc_start: 0.8392 (mmtt) cc_final: 0.7923 (mtpt)
REVERT: A  701 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8158 (mt-10)
REVERT: B   21 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8514 (t)
REVERT: B   66 LYS cc_start: 0.8747 (tppt) cc_final: 0.8078 (mttm)
REVERT: B   73 ASP cc_start: 0.8223 (t0) cc_final: 0.7793 (t0)
REVERT: B  134 ARG cc_start: 0.8300 (mtt90) cc_final: 0.7610 (mtm-85)
REVERT: B  194 LEU cc_start: 0.8071 (tp) cc_final: 0.7849 (mp)
REVERT: B  247 TYR cc_start: 0.8291 (m-10) cc_final: 0.8028 (m-10)
REVERT: B  303 GLU cc_start: 0.8200 (mp0) cc_final: 0.7956 (mp0)
REVERT: B  350 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.5910 (tp)
REVERT: B  369 LYS cc_start: 0.8272 (mmtt) cc_final: 0.7805 (mttm)
REVERT: B  580 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8177 (mtpt)
REVERT: B  590 LYS cc_start: 0.5581 (OUTLIER) cc_final: 0.5311 (pttp)
REVERT: B  714 ARG cc_start: 0.8337 (mtm-85) cc_final: 0.7885 (mtp-110)
  outliers start: 45
  outliers final: 21
  residues processed: 213
  average time/residue: 0.0953
  time to fit residues: 28.8385
Evaluate side-chains
  182 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 155
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  199 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  495 ASP
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  703 MET
Chi-restraints excluded: chain B residue   21 THR
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  495 ASP
Chi-restraints excluded: chain B residue  529 ILE
Chi-restraints excluded: chain B residue  541 GLU
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  695 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 32 optimal weight:    0.0870
   chunk 10 optimal weight:    0.6980
   chunk 128 optimal weight:    0.2980
   chunk 96 optimal weight:    0.0870
   chunk 42 optimal weight:    0.9990
   chunk 118 optimal weight:    0.7980
   chunk 65 optimal weight:    0.4980
   chunk 119 optimal weight:    0.9980
   chunk 94 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   overall best weight:    0.3336

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

Flipped N/Q/H residues before XYZ refinement:
A 135 HIS
A 160 HIS
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 656 HIS
B 160 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.152094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.118482 restraints weight = 14187.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.26
r_work: 0.3309 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10400  Z= 0.118
  Angle     :  0.537   9.861  14136  Z= 0.279
  Chirality :  0.041   0.190   1718
  Planarity :  0.004   0.045   1758
  Dihedral  :  4.423  55.381   1426
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 13.55 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.23), residues: 1322
  helix:  0.35 (0.18), residues: 866
  sheet: -3.41 (0.66), residues: 50
  loop : -2.69 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 677 
 TYR   0.018   0.001   TYR A 247 
 PHE   0.021   0.001   PHE A 122 
 TRP   0.007   0.001   TRP B 482 
 HIS   0.010   0.001   HIS A 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (10400)
  covalent geometry    : angle       0.53743 (14136)
  hydrogen bonds       : bond        0.03937 (  570)
  hydrogen bonds       : angle       4.06360 ( 1674)

*********************** 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
  194 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 161
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 ASP cc_start: 0.7775 (t0) cc_final: 0.7307 (t0)
REVERT: A   78 TYR cc_start: 0.6415 (t80) cc_final: 0.5954 (t80)
REVERT: A  119 SER cc_start: 0.9069 (t) cc_final: 0.8682 (p)
REVERT: A  269 ILE cc_start: 0.8385 (pt) cc_final: 0.7971 (pt)
REVERT: A  273 ILE cc_start: 0.8955 (mt) cc_final: 0.8714 (mt)
REVERT: A  303 GLU cc_start: 0.8264 (mp0) cc_final: 0.7948 (mp0)
REVERT: A  345 LEU cc_start: 0.6531 (mt) cc_final: 0.6176 (mt)
REVERT: A  350 LEU cc_start: 0.5775 (OUTLIER) cc_final: 0.5262 (pt)
REVERT: A  369 LYS cc_start: 0.7885 (mmtt) cc_final: 0.7410 (mttm)
REVERT: A  385 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7351 (t80)
REVERT: A  560 ASP cc_start: 0.8518 (m-30) cc_final: 0.8311 (m-30)
REVERT: A  580 LYS cc_start: 0.8355 (mmtt) cc_final: 0.7874 (mtpt)
REVERT: B   50 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6774 (tt)
REVERT: B   66 LYS cc_start: 0.8638 (tppt) cc_final: 0.7980 (mttm)
REVERT: B   73 ASP cc_start: 0.8282 (t0) cc_final: 0.7896 (t0)
REVERT: B  134 ARG cc_start: 0.8290 (mtt90) cc_final: 0.7458 (mtp180)
REVERT: B  194 LEU cc_start: 0.8007 (tp) cc_final: 0.7796 (mp)
REVERT: B  247 TYR cc_start: 0.8277 (m-10) cc_final: 0.8045 (m-10)
REVERT: B  303 GLU cc_start: 0.8256 (mp0) cc_final: 0.8053 (mp0)
REVERT: B  350 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.6122 (tp)
REVERT: B  369 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7676 (mttm)
REVERT: B  398 PHE cc_start: 0.7484 (m-80) cc_final: 0.7075 (m-80)
REVERT: B  580 LYS cc_start: 0.8426 (mmtt) cc_final: 0.8106 (mtpt)
REVERT: B  590 LYS cc_start: 0.5574 (OUTLIER) cc_final: 0.5337 (pttp)
REVERT: B  714 ARG cc_start: 0.8314 (mtm-85) cc_final: 0.7856 (mtp-110)
  outliers start: 33
  outliers final: 16
  residues processed: 186
  average time/residue: 0.0927
  time to fit residues: 24.4716
Evaluate side-chains
  170 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 149
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  495 ASP
Chi-restraints excluded: chain A residue  565 CYS
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  366 SER
Chi-restraints excluded: chain B residue  529 ILE
Chi-restraints excluded: chain B residue  590 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 127 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9980
   chunk 128 optimal weight:    0.4980
   chunk 55 optimal weight:    0.9990
   chunk 117 optimal weight:    1.9990
   chunk 112 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 160 HIS
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 656 HIS
A 731 ASN
B 160 HIS
B 656 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.147485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.115541 restraints weight = 14425.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 1.97
r_work: 0.3245 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.3651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10400  Z= 0.162
  Angle     :  0.561   7.599  14136  Z= 0.292
  Chirality :  0.043   0.174   1718
  Planarity :  0.004   0.058   1758
  Dihedral  :  4.585  55.747   1426
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.67 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 14.35 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.24), residues: 1322
  helix:  0.60 (0.18), residues: 868
  sheet: -3.18 (0.71), residues: 50
  loop : -2.56 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 576 
 TYR   0.016   0.001   TYR A 247 
 PHE   0.015   0.001   PHE A 115 
 TRP   0.006   0.001   TRP A 518 
 HIS   0.010   0.002   HIS B 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (10400)
  covalent geometry    : angle       0.56095 (14136)
  hydrogen bonds       : bond        0.03892 (  570)
  hydrogen bonds       : angle       3.97043 ( 1674)

*********************** 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
  193 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 154
  time to evaluate  : 0.385 
Fit side-chains
REVERT: A   73 ASP cc_start: 0.7813 (t0) cc_final: 0.7330 (t0)
REVERT: A   78 TYR cc_start: 0.6634 (t80) cc_final: 0.6057 (t80)
REVERT: A  119 SER cc_start: 0.9142 (t) cc_final: 0.8763 (p)
REVERT: A  269 ILE cc_start: 0.8273 (pt) cc_final: 0.7916 (pt)
REVERT: A  273 ILE cc_start: 0.8962 (mt) cc_final: 0.8705 (mt)
REVERT: A  350 LEU cc_start: 0.5967 (OUTLIER) cc_final: 0.5482 (tp)
REVERT: A  369 LYS cc_start: 0.7933 (mmtt) cc_final: 0.7514 (mttm)
REVERT: A  385 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7517 (t80)
REVERT: A  398 PHE cc_start: 0.7642 (m-80) cc_final: 0.7409 (m-80)
REVERT: A  560 ASP cc_start: 0.8678 (m-30) cc_final: 0.8450 (m-30)
REVERT: A  580 LYS cc_start: 0.8422 (mmtt) cc_final: 0.7992 (mtpt)
REVERT: B   66 LYS cc_start: 0.8622 (tppt) cc_final: 0.8356 (mttm)
REVERT: B   73 ASP cc_start: 0.8350 (t0) cc_final: 0.7481 (m-30)
REVERT: B  134 ARG cc_start: 0.8308 (mtt90) cc_final: 0.7542 (mtp180)
REVERT: B  194 LEU cc_start: 0.8008 (tp) cc_final: 0.7745 (mp)
REVERT: B  247 TYR cc_start: 0.8173 (m-10) cc_final: 0.7904 (m-10)
REVERT: B  273 ILE cc_start: 0.9087 (mm) cc_final: 0.8866 (mp)
REVERT: B  303 GLU cc_start: 0.8293 (mp0) cc_final: 0.8063 (mp0)
REVERT: B  350 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6267 (tp)
REVERT: B  369 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7634 (mttm)
REVERT: B  398 PHE cc_start: 0.7554 (m-80) cc_final: 0.7222 (m-80)
REVERT: B  580 LYS cc_start: 0.8482 (mmtt) cc_final: 0.8118 (mtpt)
REVERT: B  590 LYS cc_start: 0.5426 (OUTLIER) cc_final: 0.5205 (pttp)
REVERT: B  714 ARG cc_start: 0.8342 (mtm-85) cc_final: 0.7818 (mtp-110)
  outliers start: 39
  outliers final: 24
  residues processed: 184
  average time/residue: 0.0983
  time to fit residues: 25.4358
Evaluate side-chains
  162 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 134
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  495 ASP
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  540 GLU
Chi-restraints excluded: chain A residue  565 CYS
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  703 MET
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  495 ASP
Chi-restraints excluded: chain B residue  529 ILE
Chi-restraints excluded: chain B residue  541 GLU
Chi-restraints excluded: chain B residue  590 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 93 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 106 optimal weight:    3.9990
   chunk 95 optimal weight:    0.7980
   chunk 119 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0870
   chunk 14 optimal weight:    0.0470
   chunk 112 optimal weight:    0.9980
   overall best weight:    0.4456

-------------------------------------------------------------------------------
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 160 HIS
B 289 ASN
B 656 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.148890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.117154 restraints weight = 14274.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.98
r_work: 0.3271 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10400  Z= 0.121
  Angle     :  0.531   7.541  14136  Z= 0.278
  Chirality :  0.041   0.172   1718
  Planarity :  0.004   0.054   1758
  Dihedral  :  4.565  54.846   1426
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.15 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.24), residues: 1322
  helix:  0.81 (0.18), residues: 870
  sheet: -3.07 (0.73), residues: 50
  loop : -2.41 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 576 
 TYR   0.015   0.001   TYR A 247 
 PHE   0.014   0.001   PHE B 667 
 TRP   0.006   0.001   TRP B 482 
 HIS   0.010   0.002   HIS B 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (10400)
  covalent geometry    : angle       0.53146 (14136)
  hydrogen bonds       : bond        0.03584 (  570)
  hydrogen bonds       : angle       3.86656 ( 1674)

*********************** 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
  184 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 147
  time to evaluate  : 0.421 
Fit side-chains
REVERT: A   73 ASP cc_start: 0.7755 (t0) cc_final: 0.7543 (t0)
REVERT: A   77 LYS cc_start: 0.7954 (pttm) cc_final: 0.6896 (tptt)
REVERT: A  119 SER cc_start: 0.9087 (t) cc_final: 0.8633 (p)
REVERT: A  269 ILE cc_start: 0.8274 (pt) cc_final: 0.7767 (pt)
REVERT: A  273 ILE cc_start: 0.8935 (mt) cc_final: 0.8637 (mp)
REVERT: A  350 LEU cc_start: 0.6007 (OUTLIER) cc_final: 0.5511 (tp)
REVERT: A  369 LYS cc_start: 0.7878 (mmtt) cc_final: 0.7453 (mttm)
REVERT: A  385 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7547 (t80)
REVERT: A  432 MET cc_start: 0.8008 (tpp) cc_final: 0.7759 (tpp)
REVERT: A  560 ASP cc_start: 0.8620 (m-30) cc_final: 0.8394 (m-30)
REVERT: A  580 LYS cc_start: 0.8432 (mmtt) cc_final: 0.7985 (mtpt)
REVERT: B   66 LYS cc_start: 0.8584 (tppt) cc_final: 0.8349 (mttm)
REVERT: B   73 ASP cc_start: 0.8290 (t0) cc_final: 0.7437 (m-30)
REVERT: B  134 ARG cc_start: 0.8246 (mtt90) cc_final: 0.7497 (mtp180)
REVERT: B  247 TYR cc_start: 0.8186 (m-10) cc_final: 0.7908 (m-10)
REVERT: B  273 ILE cc_start: 0.9047 (mm) cc_final: 0.8810 (mp)
REVERT: B  303 GLU cc_start: 0.8292 (mp0) cc_final: 0.7911 (mp0)
REVERT: B  350 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6156 (tp)
REVERT: B  369 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7606 (mttm)
REVERT: B  398 PHE cc_start: 0.7536 (m-80) cc_final: 0.7276 (m-80)
REVERT: B  580 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8117 (mtpt)
REVERT: B  590 LYS cc_start: 0.5376 (OUTLIER) cc_final: 0.5159 (pttp)
REVERT: B  714 ARG cc_start: 0.8354 (mtm-85) cc_final: 0.7819 (mtp180)
  outliers start: 37
  outliers final: 26
  residues processed: 176
  average time/residue: 0.0949
  time to fit residues: 23.7293
Evaluate side-chains
  170 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 140
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  495 ASP
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  540 GLU
Chi-restraints excluded: chain A residue  565 CYS
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  724 ASP
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  529 ILE
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  666 SER
Chi-restraints excluded: chain B residue  668 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 90 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 69 optimal weight:    9.9990
   chunk 44 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 121 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 656 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.147987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.115179 restraints weight = 14476.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 2.10
r_work: 0.3212 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.3990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10400  Z= 0.150
  Angle     :  0.542   6.867  14136  Z= 0.284
  Chirality :  0.042   0.160   1718
  Planarity :  0.004   0.062   1758
  Dihedral  :  4.650  56.089   1426
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.75 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 15.51 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.24), residues: 1322
  helix:  0.96 (0.18), residues: 866
  sheet: -2.94 (0.74), residues: 50
  loop : -2.38 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 576 
 TYR   0.013   0.001   TYR B 371 
 PHE   0.015   0.001   PHE B 667 
 TRP   0.005   0.001   TRP B 482 
 HIS   0.010   0.002   HIS B 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (10400)
  covalent geometry    : angle       0.54247 (14136)
  hydrogen bonds       : bond        0.03659 (  570)
  hydrogen bonds       : angle       3.85830 ( 1674)

*********************** 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
  189 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 148
  time to evaluate  : 0.319 
Fit side-chains
REVERT: A   73 ASP cc_start: 0.7737 (t0) cc_final: 0.7484 (t0)
REVERT: A   77 LYS cc_start: 0.8022 (pttm) cc_final: 0.6990 (tptt)
REVERT: A   78 TYR cc_start: 0.6775 (t80) cc_final: 0.6068 (t80)
REVERT: A  119 SER cc_start: 0.9164 (t) cc_final: 0.8733 (p)
REVERT: A  247 TYR cc_start: 0.8270 (m-10) cc_final: 0.8033 (m-10)
REVERT: A  269 ILE cc_start: 0.8250 (pt) cc_final: 0.7877 (pt)
REVERT: A  273 ILE cc_start: 0.8983 (mt) cc_final: 0.8726 (mt)
REVERT: A  303 GLU cc_start: 0.8334 (mp0) cc_final: 0.8044 (mp0)
REVERT: A  350 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5545 (tp)
REVERT: A  369 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7621 (mttm)
REVERT: A  385 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7673 (t80)
REVERT: A  580 LYS cc_start: 0.8494 (mmtt) cc_final: 0.8066 (mtpt)
REVERT: B   66 LYS cc_start: 0.8592 (tppt) cc_final: 0.8350 (mttm)
REVERT: B   73 ASP cc_start: 0.8379 (t0) cc_final: 0.7485 (m-30)
REVERT: B  100 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8325 (mm)
REVERT: B  134 ARG cc_start: 0.8312 (mtt90) cc_final: 0.7585 (mtp180)
REVERT: B  247 TYR cc_start: 0.8242 (m-10) cc_final: 0.8002 (m-10)
REVERT: B  273 ILE cc_start: 0.9078 (mm) cc_final: 0.8826 (mp)
REVERT: B  303 GLU cc_start: 0.8267 (mp0) cc_final: 0.8002 (mp0)
REVERT: B  350 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.6137 (tp)
REVERT: B  369 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7628 (mttm)
REVERT: B  405 THR cc_start: 0.9207 (m) cc_final: 0.8892 (t)
REVERT: B  580 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8223 (mtpt)
REVERT: B  590 LYS cc_start: 0.5494 (OUTLIER) cc_final: 0.5282 (pttp)
REVERT: B  714 ARG cc_start: 0.8434 (mtm-85) cc_final: 0.7928 (mtp-110)
  outliers start: 41
  outliers final: 30
  residues processed: 180
  average time/residue: 0.0966
  time to fit residues: 24.7310
Evaluate side-chains
  171 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 136
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  495 ASP
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  540 GLU
Chi-restraints excluded: chain A residue  565 CYS
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  703 MET
Chi-restraints excluded: chain A residue  724 ASP
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  495 ASP
Chi-restraints excluded: chain B residue  529 ILE
Chi-restraints excluded: chain B residue  541 GLU
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  666 SER
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  724 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 60 optimal weight:    0.5980
   chunk 110 optimal weight:    0.4980
   chunk 71 optimal weight:    0.7980
   chunk 86 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 656 HIS
B 656 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.146597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.113841 restraints weight = 14320.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.12
r_work: 0.3201 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.4121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10400  Z= 0.151
  Angle     :  0.553   8.915  14136  Z= 0.289
  Chirality :  0.041   0.174   1718
  Planarity :  0.004   0.062   1758
  Dihedral  :  4.705  55.108   1426
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.67 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 15.95 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.24), residues: 1322
  helix:  1.00 (0.18), residues: 866
  sheet: -2.84 (0.74), residues: 50
  loop : -2.30 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 576 
 TYR   0.011   0.001   TYR A  20 
 PHE   0.015   0.001   PHE B 667 
 TRP   0.005   0.001   TRP B 482 
 HIS   0.011   0.002   HIS B 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (10400)
  covalent geometry    : angle       0.55304 (14136)
  hydrogen bonds       : bond        0.03659 (  570)
  hydrogen bonds       : angle       3.86102 ( 1674)

*********************** 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
  180 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 141
  time to evaluate  : 0.358 
Fit side-chains
REVERT: A   73 ASP cc_start: 0.7770 (t0) cc_final: 0.7551 (t0)
REVERT: A   77 LYS cc_start: 0.8021 (pttm) cc_final: 0.7090 (tptt)
REVERT: A  119 SER cc_start: 0.9136 (t) cc_final: 0.8703 (p)
REVERT: A  247 TYR cc_start: 0.8250 (m-10) cc_final: 0.8014 (m-10)
REVERT: A  269 ILE cc_start: 0.8245 (pt) cc_final: 0.7713 (pt)
REVERT: A  273 ILE cc_start: 0.8989 (mt) cc_final: 0.8689 (mp)
REVERT: A  292 PHE cc_start: 0.7724 (m-80) cc_final: 0.7488 (m-10)
REVERT: A  313 ILE cc_start: 0.9184 (mm) cc_final: 0.8953 (mm)
REVERT: A  350 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5580 (tp)
REVERT: A  369 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7542 (mttm)
REVERT: A  385 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7663 (t80)
REVERT: A  580 LYS cc_start: 0.8524 (mmtt) cc_final: 0.8087 (mtpt)
REVERT: B   66 LYS cc_start: 0.8655 (tppt) cc_final: 0.8318 (mttm)
REVERT: B   73 ASP cc_start: 0.8331 (t0) cc_final: 0.7409 (m-30)
REVERT: B  100 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8337 (mm)
REVERT: B  134 ARG cc_start: 0.8335 (mtt90) cc_final: 0.7619 (mtp180)
REVERT: B  247 TYR cc_start: 0.8253 (m-10) cc_final: 0.7965 (m-10)
REVERT: B  273 ILE cc_start: 0.9051 (mm) cc_final: 0.8786 (mp)
REVERT: B  303 GLU cc_start: 0.8252 (mp0) cc_final: 0.7978 (mp0)
REVERT: B  350 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.5989 (tp)
REVERT: B  369 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7640 (mttm)
REVERT: B  405 THR cc_start: 0.9193 (m) cc_final: 0.8930 (t)
REVERT: B  580 LYS cc_start: 0.8594 (mmtt) cc_final: 0.8215 (mtpt)
REVERT: B  590 LYS cc_start: 0.5430 (OUTLIER) cc_final: 0.5218 (pttp)
REVERT: B  714 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.7909 (mtp-110)
  outliers start: 39
  outliers final: 31
  residues processed: 170
  average time/residue: 0.0977
  time to fit residues: 23.7062
Evaluate side-chains
  175 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 139
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  495 ASP
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  565 CYS
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  724 ASP
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  463 MET
Chi-restraints excluded: chain B residue  529 ILE
Chi-restraints excluded: chain B residue  541 GLU
Chi-restraints excluded: chain B residue  575 ILE
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  666 SER
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  724 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 109 optimal weight:    0.6980
   chunk 110 optimal weight:    0.4980
   chunk 93 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0970
   chunk 48 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 121 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 46 optimal weight:    0.6980
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
A 656 HIS
B 656 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.147682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.115727 restraints weight = 14458.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.12
r_work: 0.3225 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.4218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10400  Z= 0.129
  Angle     :  0.535   9.016  14136  Z= 0.280
  Chirality :  0.041   0.163   1718
  Planarity :  0.004   0.060   1758
  Dihedral  :  4.670  54.756   1426
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.82 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 16.67 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.25), residues: 1322
  helix:  1.08 (0.18), residues: 866
  sheet: -2.80 (0.75), residues: 50
  loop : -2.19 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 576 
 TYR   0.019   0.001   TYR A 371 
 PHE   0.014   0.001   PHE A 130 
 TRP   0.006   0.001   TRP B 482 
 HIS   0.011   0.001   HIS B 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (10400)
  covalent geometry    : angle       0.53491 (14136)
  hydrogen bonds       : bond        0.03521 (  570)
  hydrogen bonds       : angle       3.81323 ( 1674)

*********************** 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
  180 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 140
  time to evaluate  : 0.462 
Fit side-chains
REVERT: A   73 ASP cc_start: 0.7773 (t0) cc_final: 0.7470 (t0)
REVERT: A   77 LYS cc_start: 0.8036 (pttm) cc_final: 0.7061 (tppt)
REVERT: A  119 SER cc_start: 0.9138 (t) cc_final: 0.8687 (p)
REVERT: A  247 TYR cc_start: 0.8183 (m-10) cc_final: 0.7944 (m-10)
REVERT: A  269 ILE cc_start: 0.8169 (pt) cc_final: 0.7796 (pt)
REVERT: A  273 ILE cc_start: 0.8941 (mt) cc_final: 0.8676 (mt)
REVERT: A  313 ILE cc_start: 0.9178 (mm) cc_final: 0.8941 (mm)
REVERT: A  350 LEU cc_start: 0.5925 (OUTLIER) cc_final: 0.5444 (tp)
REVERT: A  369 LYS cc_start: 0.7854 (mmtt) cc_final: 0.7398 (mttm)
REVERT: A  385 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7583 (t80)
REVERT: A  580 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8042 (mtpt)
REVERT: B   66 LYS cc_start: 0.8622 (tppt) cc_final: 0.8297 (mttm)
REVERT: B   73 ASP cc_start: 0.8214 (t0) cc_final: 0.7275 (m-30)
REVERT: B  100 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8270 (mm)
REVERT: B  134 ARG cc_start: 0.8297 (mtt90) cc_final: 0.7561 (mtp180)
REVERT: B  247 TYR cc_start: 0.8202 (m-10) cc_final: 0.7897 (m-10)
REVERT: B  273 ILE cc_start: 0.8998 (mm) cc_final: 0.8721 (mp)
REVERT: B  303 GLU cc_start: 0.8285 (mp0) cc_final: 0.8026 (mp0)
REVERT: B  350 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.5986 (tp)
REVERT: B  369 LYS cc_start: 0.8138 (mmtt) cc_final: 0.7625 (mttm)
REVERT: B  405 THR cc_start: 0.9153 (m) cc_final: 0.8869 (t)
REVERT: B  580 LYS cc_start: 0.8541 (mmtt) cc_final: 0.8135 (mtpt)
REVERT: B  590 LYS cc_start: 0.5448 (OUTLIER) cc_final: 0.5246 (pttp)
REVERT: B  714 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.7880 (mtp-110)
  outliers start: 40
  outliers final: 31
  residues processed: 169
  average time/residue: 0.0992
  time to fit residues: 23.5913
Evaluate side-chains
  173 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 137
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  495 ASP
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  565 CYS
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  724 ASP
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  463 MET
Chi-restraints excluded: chain B residue  495 ASP
Chi-restraints excluded: chain B residue  529 ILE
Chi-restraints excluded: chain B residue  575 ILE
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  666 SER
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  724 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 88 optimal weight:    0.4980
   chunk 101 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 120 optimal weight:    0.0010
   chunk 71 optimal weight:    0.6980
   chunk 27 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   overall best weight:    0.4986

-------------------------------------------------------------------------------
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 656 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.147579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.115727 restraints weight = 14496.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 2.12
r_work: 0.3217 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3086 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.4292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10400  Z= 0.129
  Angle     :  0.543  10.794  14136  Z= 0.283
  Chirality :  0.041   0.163   1718
  Planarity :  0.004   0.060   1758
  Dihedral  :  4.663  55.172   1426
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.82 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 17.02 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.25), residues: 1322
  helix:  1.14 (0.18), residues: 866
  sheet: -2.76 (0.75), residues: 50
  loop : -2.10 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 576 
 TYR   0.020   0.001   TYR A 371 
 PHE   0.013   0.001   PHE A 398 
 TRP   0.006   0.001   TRP A 482 
 HIS   0.011   0.002   HIS B 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10400)
  covalent geometry    : angle       0.54287 (14136)
  hydrogen bonds       : bond        0.03513 (  570)
  hydrogen bonds       : angle       3.79740 ( 1674)

*********************** 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
  181 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 142
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A   73 ASP cc_start: 0.7754 (t0) cc_final: 0.7472 (t0)
REVERT: A   77 LYS cc_start: 0.8064 (pttm) cc_final: 0.7084 (tppt)
REVERT: A  247 TYR cc_start: 0.8127 (m-10) cc_final: 0.7904 (m-10)
REVERT: A  269 ILE cc_start: 0.8135 (pt) cc_final: 0.7764 (pt)
REVERT: A  273 ILE cc_start: 0.8918 (mt) cc_final: 0.8644 (mt)
REVERT: A  313 ILE cc_start: 0.9181 (mm) cc_final: 0.8955 (mm)
REVERT: A  350 LEU cc_start: 0.5892 (OUTLIER) cc_final: 0.5422 (tp)
REVERT: A  369 LYS cc_start: 0.7799 (mmtt) cc_final: 0.7375 (mttm)
REVERT: A  385 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7618 (t80)
REVERT: A  580 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8056 (mtpt)
REVERT: B   66 LYS cc_start: 0.8617 (tppt) cc_final: 0.8299 (mttm)
REVERT: B   73 ASP cc_start: 0.8235 (t0) cc_final: 0.7378 (m-30)
REVERT: B  134 ARG cc_start: 0.8301 (mtt90) cc_final: 0.7564 (mtp180)
REVERT: B  247 TYR cc_start: 0.8195 (m-10) cc_final: 0.7863 (m-10)
REVERT: B  273 ILE cc_start: 0.8994 (mm) cc_final: 0.8718 (mp)
REVERT: B  303 GLU cc_start: 0.8289 (mp0) cc_final: 0.8030 (mp0)
REVERT: B  350 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.6069 (tp)
REVERT: B  369 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7650 (mttm)
REVERT: B  405 THR cc_start: 0.9133 (m) cc_final: 0.8860 (t)
REVERT: B  414 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7738 (tm-30)
REVERT: B  580 LYS cc_start: 0.8552 (mmtt) cc_final: 0.8144 (mtpt)
REVERT: B  714 ARG cc_start: 0.8436 (mtm-85) cc_final: 0.7876 (mtp-110)
  outliers start: 39
  outliers final: 30
  residues processed: 170
  average time/residue: 0.0982
  time to fit residues: 23.8903
Evaluate side-chains
  175 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 142
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  495 ASP
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  565 CYS
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  724 ASP
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  463 MET
Chi-restraints excluded: chain B residue  529 ILE
Chi-restraints excluded: chain B residue  575 ILE
Chi-restraints excluded: chain B residue  666 SER
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  724 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 22 optimal weight:    0.0770
   chunk 114 optimal weight:    0.5980
   chunk 107 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0970
   chunk 28 optimal weight:    0.9980
   chunk 102 optimal weight:    1.9990
   chunk 125 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 88 optimal weight:    0.0670
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.2874

-------------------------------------------------------------------------------
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 656 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.149732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.117785 restraints weight = 14323.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.10
r_work: 0.3260 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.4305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10400  Z= 0.110
  Angle     :  0.527   9.891  14136  Z= 0.275
  Chirality :  0.040   0.163   1718
  Planarity :  0.004   0.056   1758
  Dihedral  :  4.573  54.210   1426
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 18.09 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.25), residues: 1322
  helix:  1.27 (0.18), residues: 864
  sheet: -2.80 (0.75), residues: 50
  loop : -2.05 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 576 
 TYR   0.015   0.001   TYR A 371 
 PHE   0.015   0.001   PHE A 398 
 TRP   0.008   0.001   TRP A 482 
 HIS   0.011   0.001   HIS B 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (10400)
  covalent geometry    : angle       0.52666 (14136)
  hydrogen bonds       : bond        0.03325 (  570)
  hydrogen bonds       : angle       3.72531 ( 1674)

********************** 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
  175 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 147
  time to evaluate  : 0.425 
Fit side-chains
REVERT: A   73 ASP cc_start: 0.7731 (t0) cc_final: 0.7402 (m-30)
REVERT: A   77 LYS cc_start: 0.8030 (pttm) cc_final: 0.7128 (tptt)
REVERT: A  247 TYR cc_start: 0.8108 (m-10) cc_final: 0.7882 (m-10)
REVERT: A  269 ILE cc_start: 0.8255 (pt) cc_final: 0.7898 (pt)
REVERT: A  273 ILE cc_start: 0.8888 (mt) cc_final: 0.8611 (mt)
REVERT: A  313 ILE cc_start: 0.9176 (mm) cc_final: 0.8963 (mm)
REVERT: A  350 LEU cc_start: 0.5866 (OUTLIER) cc_final: 0.5398 (tp)
REVERT: A  369 LYS cc_start: 0.7684 (mmtt) cc_final: 0.7292 (mttm)
REVERT: A  385 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7669 (t80)
REVERT: A  580 LYS cc_start: 0.8463 (mmtt) cc_final: 0.8040 (mtpt)
REVERT: B   66 LYS cc_start: 0.8590 (tppt) cc_final: 0.8277 (mttm)
REVERT: B   73 ASP cc_start: 0.8199 (t0) cc_final: 0.7379 (m-30)
REVERT: B  134 ARG cc_start: 0.8277 (mtt90) cc_final: 0.7555 (mtm-85)
REVERT: B  247 TYR cc_start: 0.8163 (m-10) cc_final: 0.7869 (m-10)
REVERT: B  273 ILE cc_start: 0.8946 (mm) cc_final: 0.8670 (mp)
REVERT: B  303 GLU cc_start: 0.8253 (mp0) cc_final: 0.7990 (mp0)
REVERT: B  350 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.5968 (tp)
REVERT: B  369 LYS cc_start: 0.8131 (mmtt) cc_final: 0.7622 (mttm)
REVERT: B  414 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7722 (tm-30)
REVERT: B  580 LYS cc_start: 0.8532 (mmtt) cc_final: 0.8127 (mtpt)
REVERT: B  714 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.7881 (mtp-110)
  outliers start: 28
  outliers final: 23
  residues processed: 165
  average time/residue: 0.0962
  time to fit residues: 22.6022
Evaluate side-chains
  168 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 142
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  495 ASP
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  565 CYS
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  529 ILE
Chi-restraints excluded: chain B residue  666 SER
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  724 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0670
   chunk 70 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 125 optimal weight:    0.0670
   chunk 119 optimal weight:    0.6980
   chunk 96 optimal weight:    3.9990
   chunk 57 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.4656

-------------------------------------------------------------------------------
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 656 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.148525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.116882 restraints weight = 14501.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 2.20
r_work: 0.3226 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3094 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.4348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10400  Z= 0.125
  Angle     :  0.537   9.765  14136  Z= 0.282
  Chirality :  0.041   0.169   1718
  Planarity :  0.004   0.060   1758
  Dihedral  :  4.607  54.584   1426
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.37 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.74 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.25), residues: 1322
  helix:  1.28 (0.18), residues: 864
  sheet: -2.70 (0.75), residues: 50
  loop : -2.01 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 576 
 TYR   0.015   0.001   TYR A 371 
 PHE   0.015   0.001   PHE A 130 
 TRP   0.006   0.001   TRP B 482 
 HIS   0.011   0.001   HIS B 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (10400)
  covalent geometry    : angle       0.53724 (14136)
  hydrogen bonds       : bond        0.03396 (  570)
  hydrogen bonds       : angle       3.73194 ( 1674)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2933.48 seconds
wall clock time: 50 minutes 48.91 seconds (3048.91 seconds total)