Starting phenix.real_space_refine
on Wed Sep 17 21:40:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ask_43817/09_2025/9ask_43817.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ask_43817/09_2025/9ask_43817.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ask_43817/09_2025/9ask_43817.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ask_43817/09_2025/9ask_43817.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ask_43817/09_2025/9ask_43817.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ask_43817/09_2025/9ask_43817.map"
  }
  resolution = 3.6
  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=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      74      5.16       5
     C    7414      2.51       5
     N    1978      2.21       5
     O    2098      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11564
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 741, 5782
          Classifications: {'peptide': 741}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 21, 'TRANS': 719}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 56
          Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "B"
      Number of atoms: 5782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 741, 5782
          Classifications: {'peptide': 741}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 21, 'TRANS': 719}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 56
          Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 23
  Time building chain proxies: 3.22, per 1000 atoms: 0.28
  Number of scatterers: 11564
  At special positions: 0
  Unit cell: (153.64, 102.12, 84.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      74     16.00
     O    2098      8.00
     N    1978      7.00
     C    7414      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: 0.95
  Conformation dependent library (CDL) restraints added in 730.8 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2784

  Finding SS restraints...
    Secondary structure from input PDB file:
      75 helices and 10 sheets defined
      56.4% alpha, 7.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 77 through 88
    Processing helix  chain 'A' and resid 93 through 102
    Processing helix  chain 'A' and resid 116 through 120
      removed outlier: 3.740A  pdb=" N   GLY A 120 " --> pdb=" O   THR A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 136
      removed outlier: 4.062A  pdb=" N   ALA A 125 " --> pdb=" O   LYS A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 162
    Processing helix  chain 'A' and resid 191 through 204
      removed outlier: 3.870A  pdb=" N   GLY A 196 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLU A 204 " --> pdb=" O   ARG A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 222
      removed outlier: 3.910A  pdb=" N   GLY A 222 " --> pdb=" O   HIS A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 245
      removed outlier: 3.697A  pdb=" N   LEU A 230 " --> pdb=" O   ARG A 226 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ALA A 245 " --> pdb=" O   THR A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 325 through 335
      removed outlier: 3.968A  pdb=" N   LEU A 329 " --> pdb=" O   HIS A 325 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   CYS A 330 " --> pdb=" O   VAL A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 365
      removed outlier: 4.039A  pdb=" N   GLU A 351 " --> pdb=" O   LYS A 347 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   ASN A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   HIS A 365 " --> pdb=" O   PHE A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 394
    Processing helix  chain 'A' and resid 402 through 407
      removed outlier: 3.724A  pdb=" N   LYS A 407 " --> pdb=" O   SER A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 412
    Processing helix  chain 'A' and resid 423 through 435
      removed outlier: 3.512A  pdb=" N   ILE A 427 " --> pdb=" O   GLU A 423 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLN A 434 " --> pdb=" O   GLY A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 449
      removed outlier: 3.504A  pdb=" N   LEU A 446 " --> pdb=" O   THR A 443 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   SER A 448 " --> pdb=" O   THR A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 479
      removed outlier: 3.720A  pdb=" N   GLN A 476 " --> pdb=" O   LEU A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 510
      removed outlier: 4.129A  pdb=" N   LYS A 503 " --> pdb=" O   SER A 499 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ALA A 506 " --> pdb=" O   SER A 502 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   LEU A 507 " --> pdb=" O   LYS A 503 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   LEU A 508 " --> pdb=" O   GLY A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 528 through 540
      removed outlier: 4.307A  pdb=" N   ARG A 533 " --> pdb=" O   GLY A 529 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ALA A 534 " --> pdb=" O   SER A 530 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU A 536 " --> pdb=" O   ILE A 532 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ILE A 538 " --> pdb=" O   ALA A 534 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   VAL A 540 " --> pdb=" O   LEU A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 555
      removed outlier: 3.559A  pdb=" N   ALA A 554 " --> pdb=" O   MET A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 563
      removed outlier: 3.635A  pdb=" N   MET A 563 " --> pdb=" O   LEU A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 592
      removed outlier: 3.609A  pdb=" N   VAL A 586 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   MET A 587 " --> pdb=" O   GLU A 583 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   TRP A 588 " --> pdb=" O   ALA A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 622
      removed outlier: 3.540A  pdb=" N   LEU A 619 " --> pdb=" O   GLY A 615 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   SER A 620 " --> pdb=" O   SER A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 636
      removed outlier: 3.671A  pdb=" N   LEU A 629 " --> pdb=" O   PRO A 625 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   ASP A 630 " --> pdb=" O   ALA A 626 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA A 633 " --> pdb=" O   LEU A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 639
      No H-bonds generated for 'chain 'A' and resid 637 through 639'
    Processing helix  chain 'A' and resid 647 through 653
    Processing helix  chain 'A' and resid 665 through 676
    Processing helix  chain 'A' and resid 679 through 687
      removed outlier: 4.055A  pdb=" N   VAL A 683 " --> pdb=" O   SER A 679 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA A 684 " --> pdb=" O   MET A 680 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   GLU A 685 " --> pdb=" O   LYS A 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 730
      removed outlier: 3.675A  pdb=" N   ARG A 718 " --> pdb=" O   ALA A 714 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 733 through 742
    Processing helix  chain 'A' and resid 744 through 769
      removed outlier: 3.995A  pdb=" N   SER A 754 " --> pdb=" O   SER A 750 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL A 757 " --> pdb=" O   GLN A 753 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   TYR A 758 " --> pdb=" O   SER A 754 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   VAL A 764 " --> pdb=" O   GLY A 760 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 779
    Processing helix  chain 'A' and resid 780 through 788
      removed outlier: 3.506A  pdb=" N   LEU A 785 " --> pdb=" O   PHE A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 795 through 799
    Processing helix  chain 'A' and resid 807 through 813
    Processing helix  chain 'A' and resid 817 through 822
      removed outlier: 3.531A  pdb=" N   ALA A 822 " --> pdb=" O   VAL A 818 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 827 through 835
      removed outlier: 4.141A  pdb=" N   VAL A 831 " --> pdb=" O   VAL A 827 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ILE A 832 " --> pdb=" O   GLU A 828 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 871 through 890
      removed outlier: 3.730A  pdb=" N   LEU A 887 " --> pdb=" O   ALA A 883 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   GLN A 888 " --> pdb=" O   ARG A 884 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ASP A 890 " --> pdb=" O   ILE A 886 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 87
    Processing helix  chain 'B' and resid 94 through 101
    Processing helix  chain 'B' and resid 116 through 119
    Processing helix  chain 'B' and resid 120 through 136
      removed outlier: 4.488A  pdb=" N   VAL B 124 " --> pdb=" O   GLY B 120 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ALA B 125 " --> pdb=" O   LYS B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 162
    Processing helix  chain 'B' and resid 191 through 204
      removed outlier: 3.827A  pdb=" N   GLY B 196 " --> pdb=" O   GLU B 192 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLU B 204 " --> pdb=" O   ARG B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 222
      removed outlier: 3.931A  pdb=" N   GLY B 222 " --> pdb=" O   HIS B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 245
      removed outlier: 3.676A  pdb=" N   LEU B 230 " --> pdb=" O   ARG B 226 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ALA B 245 " --> pdb=" O   THR B 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 278
    Processing helix  chain 'B' and resid 325 through 335
      removed outlier: 3.674A  pdb=" N   LEU B 329 " --> pdb=" O   HIS B 325 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   CYS B 330 " --> pdb=" O   VAL B 326 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   THR B 333 " --> pdb=" O   LEU B 329 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   CYS B 335 " --> pdb=" O   TYR B 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 367
      removed outlier: 3.739A  pdb=" N   ASN B 363 " --> pdb=" O   ARG B 359 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   HIS B 365 " --> pdb=" O   PHE B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 394
    Processing helix  chain 'B' and resid 402 through 407
      removed outlier: 3.645A  pdb=" N   LYS B 407 " --> pdb=" O   SER B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 412
    Processing helix  chain 'B' and resid 423 through 435
      removed outlier: 3.551A  pdb=" N   ILE B 427 " --> pdb=" O   GLU B 423 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLN B 434 " --> pdb=" O   GLY B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 449
      removed outlier: 3.575A  pdb=" N   LEU B 446 " --> pdb=" O   THR B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 470 through 478
      removed outlier: 3.568A  pdb=" N   GLN B 476 " --> pdb=" O   LEU B 472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 499 through 510
      removed outlier: 4.103A  pdb=" N   LYS B 503 " --> pdb=" O   SER B 499 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ALA B 506 " --> pdb=" O   SER B 502 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   LEU B 507 " --> pdb=" O   LYS B 503 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   LEU B 508 " --> pdb=" O   GLY B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 528 through 540
      removed outlier: 4.364A  pdb=" N   ARG B 533 " --> pdb=" O   GLY B 529 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   ALA B 534 " --> pdb=" O   SER B 530 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   ILE B 538 " --> pdb=" O   ALA B 534 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   VAL B 540 " --> pdb=" O   LEU B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 546 through 555
      removed outlier: 3.541A  pdb=" N   ALA B 555 " --> pdb=" O   HIS B 551 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 563
      removed outlier: 3.654A  pdb=" N   MET B 563 " --> pdb=" O   LEU B 559 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 581 through 592
      removed outlier: 3.881A  pdb=" N   VAL B 586 " --> pdb=" O   ILE B 582 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   MET B 587 " --> pdb=" O   GLU B 583 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 622
      removed outlier: 3.524A  pdb=" N   LEU B 619 " --> pdb=" O   GLY B 615 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   SER B 620 " --> pdb=" O   SER B 616 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 624 through 635
      removed outlier: 3.655A  pdb=" N   LEU B 629 " --> pdb=" O   PRO B 625 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   ASP B 630 " --> pdb=" O   ALA B 626 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA B 633 " --> pdb=" O   LEU B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 647 through 653
    Processing helix  chain 'B' and resid 665 through 676
    Processing helix  chain 'B' and resid 679 through 687
      removed outlier: 4.047A  pdb=" N   VAL B 683 " --> pdb=" O   SER B 679 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ALA B 684 " --> pdb=" O   MET B 680 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   GLU B 685 " --> pdb=" O   LYS B 681 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 710 through 729
      removed outlier: 3.642A  pdb=" N   ARG B 718 " --> pdb=" O   ALA B 714 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 733 through 742
    Processing helix  chain 'B' and resid 744 through 769
      removed outlier: 3.981A  pdb=" N   SER B 754 " --> pdb=" O   SER B 750 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   VAL B 757 " --> pdb=" O   GLN B 753 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TYR B 758 " --> pdb=" O   SER B 754 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   VAL B 764 " --> pdb=" O   GLY B 760 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 773 through 779
    Processing helix  chain 'B' and resid 780 through 788
      removed outlier: 3.554A  pdb=" N   LEU B 785 " --> pdb=" O   PHE B 781 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   PHE B 787 " --> pdb=" O   LYS B 783 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 795 through 799
    Processing helix  chain 'B' and resid 807 through 813
    Processing helix  chain 'B' and resid 817 through 822
      removed outlier: 3.514A  pdb=" N   ALA B 822 " --> pdb=" O   VAL B 818 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 827 through 835
      removed outlier: 4.146A  pdb=" N   VAL B 831 " --> pdb=" O   VAL B 827 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ILE B 832 " --> pdb=" O   GLU B 828 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 871 through 890
      removed outlier: 3.733A  pdb=" N   LEU B 887 " --> pdb=" O   ALA B 883 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLN B 888 " --> pdb=" O   ARG B 884 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ASP B 890 " --> pdb=" O   ILE B 886 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 169
      removed outlier: 7.501A  pdb=" N   ALA A 140 " --> pdb=" O   ALA A 187 " (cutoff:3.500A)
      removed outlier: 7.763A  pdb=" N   CYS A 189 " --> pdb=" O   ALA A 140 " (cutoff:3.500A)
      removed outlier: 5.400A  pdb=" N   PHE A 142 " --> pdb=" O   CYS A 189 " (cutoff:3.500A)
      removed outlier: 5.879A  pdb=" N   LYS A 139 " --> pdb=" O   LEU A 210 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   MET A 212 " --> pdb=" O   LYS A 139 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   MET A 264 " --> pdb=" O   VAL A 215 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   VAL A 112 " --> pdb=" O   GLU A 281 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   TYR A 283 " --> pdb=" O   VAL A 112 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 309 through 312
      removed outlier: 4.047A  pdb=" N   ARG A 311 " --> pdb=" O   ILE A 302 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   LEU A 293 " --> pdb=" O   SER A 492 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   LEU A 494 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   SER A 295 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   VAL A 457 " --> pdb=" O   ILE A 493 " (cutoff:3.500A)
      removed outlier: 7.575A  pdb=" N   ILE A 495 " --> pdb=" O   VAL A 457 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   ILE A 459 " --> pdb=" O   ILE A 495 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   LEU A 341 " --> pdb=" O   ILE A 458 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 464
    Processing sheet with id=AA4, first strand: chain 'A' and resid 595 through 598
      removed outlier: 3.607A  pdb=" N   HIS A 610 " --> pdb=" O   GLN A 596 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR A 598 " --> pdb=" O   VAL A 608 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   VAL A 608 " --> pdb=" O   THR A 598 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 862 through 863
    Processing sheet with id=AA6, first strand: chain 'B' and resid 168 through 169
      removed outlier: 7.539A  pdb=" N   ALA B 140 " --> pdb=" O   ALA B 187 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   CYS B 189 " --> pdb=" O   ALA B 140 " (cutoff:3.500A)
      removed outlier: 5.443A  pdb=" N   PHE B 142 " --> pdb=" O   CYS B 189 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   VAL B 112 " --> pdb=" O   GLU B 281 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   TYR B 283 " --> pdb=" O   VAL B 112 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 309 through 312
      removed outlier: 4.041A  pdb=" N   ARG B 311 " --> pdb=" O   ILE B 302 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   VAL B 457 " --> pdb=" O   ILE B 493 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   LEU B 341 " --> pdb=" O   ILE B 458 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 463 through 464
      removed outlier: 3.512A  pdb=" N   ARG B 467 " --> pdb=" O   PHE B 464 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 595 through 598
      removed outlier: 3.573A  pdb=" N   HIS B 610 " --> pdb=" O   GLN B 596 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   THR B 598 " --> pdb=" O   VAL B 608 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL B 608 " --> pdb=" O   THR B 598 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 862 through 863

    499 hydrogen bonds defined for protein.
    1422 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.14

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3758
        1.34 -     1.46: 2552
        1.46 -     1.58: 5336
        1.58 -     1.70: 0
        1.70 -     1.82: 118
  Bond restraints: 11764
  Sorted by residual:
  bond pdb=" CA  ILE B 166 "
       pdb=" CB  ILE B 166 "
    ideal  model  delta    sigma   weight residual
    1.527  1.544 -0.017 1.31e-02 5.83e+03 1.71e+00
  bond pdb=" CB  ASN A 270 "
       pdb=" CG  ASN A 270 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 2.50e-02 1.60e+03 1.58e+00
  bond pdb=" CB  ASN B 270 "
       pdb=" CG  ASN B 270 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 2.50e-02 1.60e+03 1.52e+00
  bond pdb=" CB  ARG A 242 "
       pdb=" CG  ARG A 242 "
    ideal  model  delta    sigma   weight residual
    1.520  1.555 -0.035 3.00e-02 1.11e+03 1.38e+00
  bond pdb=" SD  MET A 477 "
       pdb=" CE  MET A 477 "
    ideal  model  delta    sigma   weight residual
    1.791  1.767  0.024 2.50e-02 1.60e+03 9.44e-01
  ... (remaining 11759 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 15638
        1.98 -     3.96: 222
        3.96 -     5.93: 38
        5.93 -     7.91: 9
        7.91 -     9.89: 5
  Bond angle restraints: 15912
  Sorted by residual:
  angle pdb=" CB  MET B 477 "
        pdb=" CG  MET B 477 "
        pdb=" SD  MET B 477 "
      ideal   model   delta    sigma   weight residual
     112.70  102.81    9.89 3.00e+00 1.11e-01 1.09e+01
  angle pdb=" CB  ARG A 242 "
        pdb=" CG  ARG A 242 "
        pdb=" CD  ARG A 242 "
      ideal   model   delta    sigma   weight residual
     111.30  117.79   -6.49 2.30e+00 1.89e-01 7.96e+00
  angle pdb=" CB  MET A 477 "
        pdb=" CG  MET A 477 "
        pdb=" SD  MET A 477 "
      ideal   model   delta    sigma   weight residual
     112.70  104.28    8.42 3.00e+00 1.11e-01 7.88e+00
  angle pdb=" CA  LEU A 233 "
        pdb=" CB  LEU A 233 "
        pdb=" CG  LEU A 233 "
      ideal   model   delta    sigma   weight residual
     116.30  125.95   -9.65 3.50e+00 8.16e-02 7.60e+00
  angle pdb=" N   VAL B 486 "
        pdb=" CA  VAL B 486 "
        pdb=" C   VAL B 486 "
      ideal   model   delta    sigma   weight residual
     111.62  109.54    2.08 7.90e-01 1.60e+00 6.95e+00
  ... (remaining 15907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.15: 5909
       18.15 -    36.30: 895
       36.30 -    54.44: 210
       54.44 -    72.59: 43
       72.59 -    90.74: 19
  Dihedral angle restraints: 7076
    sinusoidal: 2790
      harmonic: 4286
  Sorted by residual:
  dihedral pdb=" CA  ASP B 630 "
           pdb=" CB  ASP B 630 "
           pdb=" CG  ASP B 630 "
           pdb=" OD1 ASP B 630 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.49   58.49     1      2.00e+01 2.50e-03 1.15e+01
  dihedral pdb=" CA  ASP A 630 "
           pdb=" CB  ASP A 630 "
           pdb=" CG  ASP A 630 "
           pdb=" OD1 ASP A 630 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.25   58.25     1      2.00e+01 2.50e-03 1.14e+01
  dihedral pdb=" CA  LEU A 282 "
           pdb=" C   LEU A 282 "
           pdb=" N   TYR A 283 "
           pdb=" CA  TYR A 283 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.17   16.83     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 7073 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1109
       0.029 -    0.058: 512
       0.058 -    0.086: 162
       0.086 -    0.115: 74
       0.115 -    0.144: 19
  Chirality restraints: 1876
  Sorted by residual:
  chirality pdb=" CA  ASN A 270 "
            pdb=" N   ASN A 270 "
            pdb=" C   ASN A 270 "
            pdb=" CB  ASN A 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.20e-01
  chirality pdb=" CA  VAL B 732 "
            pdb=" N   VAL B 732 "
            pdb=" C   VAL B 732 "
            pdb=" CB  VAL B 732 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.97e-01
  chirality pdb=" CA  ASN B 270 "
            pdb=" N   ASN B 270 "
            pdb=" C   ASN B 270 "
            pdb=" CB  ASN B 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.88e-01
  ... (remaining 1873 not shown)

  Planarity restraints: 1990
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 513 "    0.042 5.00e-02 4.00e+02   6.26e-02 6.28e+00
        pdb=" N   PRO A 514 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 514 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 514 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 513 "   -0.041 5.00e-02 4.00e+02   6.12e-02 6.00e+00
        pdb=" N   PRO B 514 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO B 514 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 514 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 204 "   -0.011 2.00e-02 2.50e+03   2.14e-02 4.57e+00
        pdb=" C   GLU B 204 "    0.037 2.00e-02 2.50e+03
        pdb=" O   GLU B 204 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ASN B 205 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1987 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 3139
        2.80 -     3.32: 11186
        3.32 -     3.85: 19097
        3.85 -     4.37: 21988
        4.37 -     4.90: 36960
  Nonbonded interactions: 92370
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B 236 "
            pdb=" OE1 GLU B 537 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" O   ASP A 549 "
            pdb=" OG1 THR A 552 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OG1 THR B 421 "
            pdb=" NH1 ARG B 745 "
     model   vdw
     2.282 3.120
  nonbonded pdb=" OE2 GLU B 424 "
            pdb=" NH1 ARG B 745 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" OD2 ASP A 647 "
            pdb=" NH1 ARG A 784 "
     model   vdw
     2.296 3.120
  ... (remaining 92365 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: 0.02
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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.770
  Find NCS groups from input model:        0.170
  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:1.370
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6784
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      :  0.003   0.035  11764  Z= 0.122
  Angle     :  0.604   9.891  15912  Z= 0.297
  Chirality :  0.040   0.144   1876
  Planarity :  0.004   0.063   1990
  Dihedral  : 18.522  90.740   4292
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 36.10 %
    Favored  : 63.50 %
  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 aren not related in a simple way.
  whole: -1.03 (0.22), residues: 1446
  helix: -0.43 (0.20), residues: 696
  sheet: -0.02 (0.49), residues: 114
  loop : -0.97 (0.24), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 242 
 TYR   0.029   0.002   TYR A 283 
 PHE   0.025   0.001   PHE B 146 
 TRP   0.006   0.001   TRP B  95 
 HIS   0.005   0.001   HIS B 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (11764)
  covalent geometry    : angle       0.60417 (15912)
  hydrogen bonds       : bond        0.29238 (  499)
  hydrogen bonds       : angle       8.63786 ( 1422)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 238
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 LEU cc_start: 0.8185 (mm) cc_final: 0.7873 (mm)
REVERT: B  438 ARG cc_start: 0.6362 (ttm-80) cc_final: 0.6037 (ttm-80)
REVERT: B  493 ILE cc_start: 0.8725 (mt) cc_final: 0.8506 (mt)
  outliers start: 5
  outliers final: 2
  residues processed: 242
  average time/residue: 0.1156
  time to fit residues: 40.2009
Evaluate side-chains
  190 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 188
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain B residue  862 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.4980
   chunk 10 optimal weight:    0.0470
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.1980
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    0.1980
   chunk 55 optimal weight:    0.0020
   overall best weight:    0.1886

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

Flipped N/Q/H residues before XYZ refinement:
A 110 ASN
A 498 ASN
B 195 ASN
B 219 HIS
B 498 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.211425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.179393 restraints weight = 16377.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.184431 restraints weight = 9254.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.187867 restraints weight = 6311.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.190196 restraints weight = 4855.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.191746 restraints weight = 4046.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.4452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6660
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11764  Z= 0.136
  Angle     :  0.623   8.479  15912  Z= 0.311
  Chirality :  0.041   0.142   1876
  Planarity :  0.004   0.044   1990
  Dihedral  :  4.312  34.844   1583
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 32.51 %
    Favored  : 62.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.11 (0.21), residues: 1446
  helix: -0.24 (0.18), residues: 790
  sheet:  0.07 (0.44), residues: 132
  loop : -1.58 (0.25), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 311 
 TYR   0.024   0.002   TYR A 283 
 PHE   0.016   0.001   PHE A 464 
 TRP   0.009   0.001   TRP B 673 
 HIS   0.006   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (11764)
  covalent geometry    : angle       0.62329 (15912)
  hydrogen bonds       : bond        0.04806 (  499)
  hydrogen bonds       : angle       5.61241 ( 1422)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 207
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6451 (tt0)
REVERT: A  226 ARG cc_start: 0.7681 (ptp90) cc_final: 0.7385 (ptp90)
REVERT: A  264 MET cc_start: 0.6409 (mpp) cc_final: 0.6207 (mpp)
REVERT: A  483 ARG cc_start: 0.7177 (mpt-90) cc_final: 0.6642 (mtm-85)
REVERT: A  817 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8718 (p)
REVERT: A  835 ASN cc_start: 0.7708 (m110) cc_final: 0.7448 (t0)
REVERT: B  332 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6435 (tt0)
REVERT: B  493 ILE cc_start: 0.8651 (mt) cc_final: 0.8328 (mt)
REVERT: B  835 ASN cc_start: 0.7687 (m110) cc_final: 0.7440 (t0)
  outliers start: 63
  outliers final: 34
  residues processed: 248
  average time/residue: 0.1147
  time to fit residues: 40.8617
Evaluate side-chains
  219 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 184
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  303 TYR
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  535 ILE
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  659 GLU
Chi-restraints excluded: chain A residue  745 ARG
Chi-restraints excluded: chain A residue  817 THR
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain B residue  422 PHE
Chi-restraints excluded: chain B residue  470 ASP
Chi-restraints excluded: chain B residue  487 ASP
Chi-restraints excluded: chain B residue  528 THR
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain B residue  659 GLU
Chi-restraints excluded: chain B residue  662 THR
Chi-restraints excluded: chain B residue  744 ASN
Chi-restraints excluded: chain B residue  810 LEU
Chi-restraints excluded: chain B residue  831 VAL
Chi-restraints excluded: chain B residue  833 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 115 optimal weight:    0.0030
   chunk 103 optimal weight:    0.7980
   chunk 113 optimal weight:    0.9990
   chunk 130 optimal weight:    0.5980
   chunk 117 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 133 optimal weight:    0.9990
   chunk 112 optimal weight:    0.0870
   chunk 123 optimal weight:    0.6980
   chunk 22 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.4368

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

Flipped N/Q/H residues before XYZ refinement:
A 476 GLN
A 596 GLN
A 649 HIS
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 649 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4605 r_free = 0.4605 target = 0.209820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.177373 restraints weight = 16536.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.182487 restraints weight = 9492.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.185893 restraints weight = 6507.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.188258 restraints weight = 5036.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.189613 restraints weight = 4196.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.4432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6693
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11764  Z= 0.128
  Angle     :  0.589   9.790  15912  Z= 0.288
  Chirality :  0.041   0.168   1876
  Planarity :  0.004   0.040   1990
  Dihedral  :  4.097  18.691   1580
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 33.07 %
    Favored  : 62.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.97 (0.21), residues: 1446
  helix: -0.06 (0.18), residues: 808
  sheet:  0.11 (0.43), residues: 130
  loop : -1.68 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 242 
 TYR   0.024   0.002   TYR A 283 
 PHE   0.018   0.001   PHE B 343 
 TRP   0.008   0.001   TRP A 588 
 HIS   0.005   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (11764)
  covalent geometry    : angle       0.58895 (15912)
  hydrogen bonds       : bond        0.03966 (  499)
  hydrogen bonds       : angle       5.11253 ( 1422)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 196
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 MET cc_start: 0.5047 (ppp) cc_final: 0.4724 (ppp)
REVERT: A  135 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6670 (tt0)
REVERT: A  226 ARG cc_start: 0.7706 (ptp90) cc_final: 0.7350 (ptp90)
REVERT: A  307 MET cc_start: 0.4536 (mmp) cc_final: 0.4202 (mmp)
REVERT: A  308 LYS cc_start: 0.7252 (ttmm) cc_final: 0.6901 (tttm)
REVERT: A  483 ARG cc_start: 0.7212 (mpt-90) cc_final: 0.6706 (mtm-85)
REVERT: A  493 ILE cc_start: 0.8433 (mt) cc_final: 0.8198 (mt)
REVERT: A  798 ARG cc_start: 0.8282 (ttm-80) cc_final: 0.8045 (ttm110)
REVERT: A  835 ASN cc_start: 0.7807 (m110) cc_final: 0.7482 (t0)
REVERT: B  332 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6567 (tt0)
REVERT: B  493 ILE cc_start: 0.8646 (mt) cc_final: 0.8331 (mt)
REVERT: B  680 MET cc_start: 0.6168 (tpp) cc_final: 0.5942 (tpp)
REVERT: B  835 ASN cc_start: 0.7809 (m110) cc_final: 0.7472 (t0)
  outliers start: 59
  outliers final: 39
  residues processed: 236
  average time/residue: 0.1125
  time to fit residues: 38.0100
Evaluate side-chains
  220 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 181
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  303 TYR
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  535 ILE
Chi-restraints excluded: chain A residue  659 GLU
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  745 ARG
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  862 ILE
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  303 TYR
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  360 GLU
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain B residue  422 PHE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  470 ASP
Chi-restraints excluded: chain B residue  487 ASP
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain B residue  659 GLU
Chi-restraints excluded: chain B residue  724 VAL
Chi-restraints excluded: chain B residue  744 ASN
Chi-restraints excluded: chain B residue  810 LEU
Chi-restraints excluded: chain B residue  833 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9990
   chunk 146 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9980
   chunk 111 optimal weight:    0.0270
   chunk 82 optimal weight:    0.5980
   chunk 125 optimal weight:    0.8980
   overall best weight:    0.7038

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

Flipped N/Q/H residues before XYZ refinement:
A 104 GLN
A 476 GLN
A 596 GLN
B 104 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.208246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.175291 restraints weight = 16542.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.180348 restraints weight = 9489.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.183768 restraints weight = 6531.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.185883 restraints weight = 5058.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.187611 restraints weight = 4273.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.4409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6777
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11764  Z= 0.145
  Angle     :  0.592   8.763  15912  Z= 0.289
  Chirality :  0.041   0.134   1876
  Planarity :  0.004   0.037   1990
  Dihedral  :  4.187  18.611   1580
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 33.31 %
    Favored  : 60.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.01 (0.21), residues: 1446
  helix: -0.03 (0.18), residues: 812
  sheet: -0.53 (0.40), residues: 152
  loop : -1.69 (0.26), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 483 
 TYR   0.024   0.002   TYR A 283 
 PHE   0.020   0.001   PHE B 146 
 TRP   0.007   0.001   TRP A 588 
 HIS   0.007   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (11764)
  covalent geometry    : angle       0.59203 (15912)
  hydrogen bonds       : bond        0.03659 (  499)
  hydrogen bonds       : angle       4.89417 ( 1422)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 186
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6665 (tt0)
REVERT: A  226 ARG cc_start: 0.7713 (ptp90) cc_final: 0.7405 (ptp90)
REVERT: A  303 TYR cc_start: 0.6611 (OUTLIER) cc_final: 0.6072 (m-80)
REVERT: A  307 MET cc_start: 0.4339 (mmp) cc_final: 0.3960 (mmp)
REVERT: A  308 LYS cc_start: 0.7437 (ttmm) cc_final: 0.6928 (tttm)
REVERT: A  487 ASP cc_start: 0.6808 (OUTLIER) cc_final: 0.6380 (m-30)
REVERT: A  493 ILE cc_start: 0.8535 (mt) cc_final: 0.8300 (mt)
REVERT: A  835 ASN cc_start: 0.7779 (m110) cc_final: 0.7436 (t0)
REVERT: B  332 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6421 (tt0)
REVERT: B  487 ASP cc_start: 0.7086 (OUTLIER) cc_final: 0.6495 (m-30)
REVERT: B  493 ILE cc_start: 0.8744 (mt) cc_final: 0.8423 (mt)
REVERT: B  680 MET cc_start: 0.6437 (tpp) cc_final: 0.6211 (tpp)
REVERT: B  835 ASN cc_start: 0.7735 (m110) cc_final: 0.7414 (t0)
REVERT: B  889 GLN cc_start: 0.6054 (OUTLIER) cc_final: 0.5836 (pt0)
  outliers start: 76
  outliers final: 49
  residues processed: 240
  average time/residue: 0.0969
  time to fit residues: 34.3376
Evaluate side-chains
  228 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 175
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 GLN
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  303 TYR
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  422 PHE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  470 ASP
Chi-restraints excluded: chain A residue  487 ASP
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  535 ILE
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  659 GLU
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  745 ARG
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  862 ILE
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  303 TYR
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  360 GLU
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain B residue  422 PHE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  470 ASP
Chi-restraints excluded: chain B residue  487 ASP
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain B residue  659 GLU
Chi-restraints excluded: chain B residue  724 VAL
Chi-restraints excluded: chain B residue  744 ASN
Chi-restraints excluded: chain B residue  810 LEU
Chi-restraints excluded: chain B residue  833 LEU
Chi-restraints excluded: chain B residue  889 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 62 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 106 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0040
   chunk 93 optimal weight:    0.9980
   chunk 22 optimal weight:   10.0000
   chunk 132 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 109 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
A 476 GLN
B 104 GLN
** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.208293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.174962 restraints weight = 16661.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.180092 restraints weight = 9531.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.183619 restraints weight = 6555.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.185772 restraints weight = 5057.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.187162 restraints weight = 4264.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.4386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6770
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11764  Z= 0.128
  Angle     :  0.596  10.365  15912  Z= 0.287
  Chirality :  0.041   0.138   1876
  Planarity :  0.004   0.036   1990
  Dihedral  :  4.175  19.336   1580
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.50 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 33.55 %
    Favored  : 61.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.93 (0.21), residues: 1446
  helix:  0.06 (0.18), residues: 818
  sheet: -0.64 (0.42), residues: 142
  loop : -1.64 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 483 
 TYR   0.022   0.002   TYR A 283 
 PHE   0.020   0.001   PHE B 146 
 TRP   0.008   0.001   TRP A 588 
 HIS   0.007   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (11764)
  covalent geometry    : angle       0.59610 (15912)
  hydrogen bonds       : bond        0.03452 (  499)
  hydrogen bonds       : angle       4.74231 ( 1422)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 182
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 MET cc_start: 0.5231 (ppp) cc_final: 0.4537 (ppp)
REVERT: A  135 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6697 (tt0)
REVERT: A  226 ARG cc_start: 0.7717 (ptp90) cc_final: 0.7393 (ptp90)
REVERT: A  303 TYR cc_start: 0.6689 (OUTLIER) cc_final: 0.6234 (m-80)
REVERT: A  308 LYS cc_start: 0.7344 (ttmm) cc_final: 0.6807 (tttm)
REVERT: A  487 ASP cc_start: 0.6754 (OUTLIER) cc_final: 0.6311 (m-30)
REVERT: A  493 ILE cc_start: 0.8528 (mt) cc_final: 0.8294 (mt)
REVERT: A  685 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6982 (mp0)
REVERT: A  835 ASN cc_start: 0.7866 (m110) cc_final: 0.7461 (t0)
REVERT: B  332 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6363 (tt0)
REVERT: B  493 ILE cc_start: 0.8719 (mt) cc_final: 0.8385 (mt)
REVERT: B  680 MET cc_start: 0.6385 (tpp) cc_final: 0.6171 (tpp)
REVERT: B  685 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7047 (mp0)
REVERT: B  835 ASN cc_start: 0.7832 (m110) cc_final: 0.7451 (t0)
REVERT: B  889 GLN cc_start: 0.6084 (OUTLIER) cc_final: 0.5869 (pt0)
  outliers start: 68
  outliers final: 47
  residues processed: 229
  average time/residue: 0.1003
  time to fit residues: 33.8960
Evaluate side-chains
  228 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 176
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  303 TYR
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  422 PHE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  470 ASP
Chi-restraints excluded: chain A residue  487 ASP
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  535 ILE
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  659 GLU
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  685 GLU
Chi-restraints excluded: chain A residue  745 ARG
Chi-restraints excluded: chain A residue  752 GLN
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  360 GLU
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain B residue  422 PHE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  470 ASP
Chi-restraints excluded: chain B residue  487 ASP
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain B residue  643 VAL
Chi-restraints excluded: chain B residue  659 GLU
Chi-restraints excluded: chain B residue  685 GLU
Chi-restraints excluded: chain B residue  744 ASN
Chi-restraints excluded: chain B residue  810 LEU
Chi-restraints excluded: chain B residue  831 VAL
Chi-restraints excluded: chain B residue  833 LEU
Chi-restraints excluded: chain B residue  889 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 44 optimal weight:    0.0470
   chunk 124 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 5 optimal weight:    0.6980
   chunk 120 optimal weight:    0.8980
   chunk 140 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 70 optimal weight:    9.9990
   chunk 117 optimal weight:    0.6980
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
A 104 GLN
A 476 GLN
** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.206981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.173815 restraints weight = 16659.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.178901 restraints weight = 9582.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.182369 restraints weight = 6626.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.184710 restraints weight = 5131.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.186070 restraints weight = 4301.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.4377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6783
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11764  Z= 0.133
  Angle     :  0.598   9.844  15912  Z= 0.287
  Chirality :  0.041   0.137   1876
  Planarity :  0.004   0.040   1990
  Dihedral  :  4.173  18.850   1580
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  5.91 %
    Allowed  : 33.31 %
    Favored  : 60.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.21), residues: 1446
  helix:  0.08 (0.18), residues: 820
  sheet: -0.69 (0.41), residues: 142
  loop : -1.64 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 396 
 TYR   0.021   0.001   TYR A 283 
 PHE   0.020   0.001   PHE A 464 
 TRP   0.008   0.001   TRP A 588 
 HIS   0.006   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (11764)
  covalent geometry    : angle       0.59804 (15912)
  hydrogen bonds       : bond        0.03354 (  499)
  hydrogen bonds       : angle       4.64534 ( 1422)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 182
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6698 (tt0)
REVERT: A  142 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7401 (t80)
REVERT: A  226 ARG cc_start: 0.7722 (ptp90) cc_final: 0.7416 (ptp90)
REVERT: A  242 ARG cc_start: 0.7284 (ttp80) cc_final: 0.6974 (ttp80)
REVERT: A  303 TYR cc_start: 0.6748 (OUTLIER) cc_final: 0.6368 (m-80)
REVERT: A  308 LYS cc_start: 0.7312 (ttmm) cc_final: 0.6782 (tttm)
REVERT: A  487 ASP cc_start: 0.6747 (OUTLIER) cc_final: 0.6275 (m-30)
REVERT: A  493 ILE cc_start: 0.8559 (mt) cc_final: 0.8334 (mt)
REVERT: A  685 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7053 (mp0)
REVERT: A  835 ASN cc_start: 0.7829 (m110) cc_final: 0.7445 (t0)
REVERT: B  142 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7527 (t80)
REVERT: B  332 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6464 (tt0)
REVERT: B  463 ILE cc_start: 0.7385 (mm) cc_final: 0.7040 (mm)
REVERT: B  493 ILE cc_start: 0.8690 (mt) cc_final: 0.8394 (mt)
REVERT: B  685 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7014 (mp0)
REVERT: B  835 ASN cc_start: 0.7770 (m110) cc_final: 0.7415 (t0)
REVERT: B  889 GLN cc_start: 0.6085 (OUTLIER) cc_final: 0.5865 (pt0)
  outliers start: 74
  outliers final: 54
  residues processed: 232
  average time/residue: 0.1046
  time to fit residues: 35.3699
Evaluate side-chains
  239 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 178
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 GLN
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  303 TYR
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  422 PHE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  470 ASP
Chi-restraints excluded: chain A residue  487 ASP
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  535 ILE
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  659 GLU
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  685 GLU
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  745 ARG
Chi-restraints excluded: chain A residue  752 GLN
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  862 ILE
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  360 GLU
Chi-restraints excluded: chain B residue  361 PHE
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain B residue  422 PHE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  470 ASP
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  619 LEU
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain B residue  643 VAL
Chi-restraints excluded: chain B residue  659 GLU
Chi-restraints excluded: chain B residue  685 GLU
Chi-restraints excluded: chain B residue  744 ASN
Chi-restraints excluded: chain B residue  752 GLN
Chi-restraints excluded: chain B residue  810 LEU
Chi-restraints excluded: chain B residue  831 VAL
Chi-restraints excluded: chain B residue  833 LEU
Chi-restraints excluded: chain B residue  889 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 99 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 47 optimal weight:    0.4980
   chunk 6 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0870
   chunk 70 optimal weight:    8.9990
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A 476 GLN
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4572 r_free = 0.4572 target = 0.206494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.173580 restraints weight = 16629.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.178570 restraints weight = 9612.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.182024 restraints weight = 6652.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.184188 restraints weight = 5159.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.185848 restraints weight = 4345.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.4395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6792
moved from start:          0.2779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11764  Z= 0.135
  Angle     :  0.611  10.593  15912  Z= 0.293
  Chirality :  0.041   0.134   1876
  Planarity :  0.004   0.036   1990
  Dihedral  :  4.196  19.215   1580
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.29 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 32.91 %
    Favored  : 61.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.21), residues: 1446
  helix:  0.10 (0.18), residues: 818
  sheet: -0.69 (0.42), residues: 142
  loop : -1.67 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 396 
 TYR   0.021   0.001   TYR A 283 
 PHE   0.017   0.001   PHE B 146 
 TRP   0.008   0.001   TRP A 588 
 HIS   0.006   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (11764)
  covalent geometry    : angle       0.61051 (15912)
  hydrogen bonds       : bond        0.03311 (  499)
  hydrogen bonds       : angle       4.61605 ( 1422)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 184
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6756 (tt0)
REVERT: A  142 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7351 (t80)
REVERT: A  226 ARG cc_start: 0.7719 (ptp90) cc_final: 0.7404 (ptp90)
REVERT: A  303 TYR cc_start: 0.6796 (OUTLIER) cc_final: 0.6404 (m-80)
REVERT: A  308 LYS cc_start: 0.7311 (ttmm) cc_final: 0.6795 (tttm)
REVERT: A  462 PRO cc_start: 0.7965 (Cg_endo) cc_final: 0.7691 (Cg_exo)
REVERT: A  487 ASP cc_start: 0.6737 (OUTLIER) cc_final: 0.6223 (m-30)
REVERT: A  493 ILE cc_start: 0.8583 (mt) cc_final: 0.8357 (mt)
REVERT: A  640 LYS cc_start: 0.7886 (mmtm) cc_final: 0.7655 (mmtt)
REVERT: A  685 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7036 (mp0)
REVERT: A  826 ILE cc_start: 0.8310 (mt) cc_final: 0.7969 (tp)
REVERT: A  835 ASN cc_start: 0.7802 (m110) cc_final: 0.7440 (t0)
REVERT: B  142 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7577 (t80)
REVERT: B  332 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6452 (tt0)
REVERT: B  463 ILE cc_start: 0.7381 (mm) cc_final: 0.7088 (mm)
REVERT: B  493 ILE cc_start: 0.8726 (mt) cc_final: 0.8415 (mt)
REVERT: B  508 LEU cc_start: 0.8512 (mm) cc_final: 0.8289 (mm)
REVERT: B  649 HIS cc_start: 0.7529 (OUTLIER) cc_final: 0.6833 (t70)
REVERT: B  685 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7008 (mp0)
REVERT: B  717 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6683 (mmtt)
REVERT: B  835 ASN cc_start: 0.7790 (m110) cc_final: 0.7445 (t0)
  outliers start: 75
  outliers final: 56
  residues processed: 233
  average time/residue: 0.1136
  time to fit residues: 37.9108
Evaluate side-chains
  241 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 177
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  220 MET
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  303 TYR
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  422 PHE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  470 ASP
Chi-restraints excluded: chain A residue  487 ASP
Chi-restraints excluded: chain A residue  530 SER
Chi-restraints excluded: chain A residue  535 ILE
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  659 GLU
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  685 GLU
Chi-restraints excluded: chain A residue  717 LYS
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  745 ARG
Chi-restraints excluded: chain A residue  752 GLN
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  862 ILE
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  360 GLU
Chi-restraints excluded: chain B residue  361 PHE
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain B residue  422 PHE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  470 ASP
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  619 LEU
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain B residue  643 VAL
Chi-restraints excluded: chain B residue  649 HIS
Chi-restraints excluded: chain B residue  659 GLU
Chi-restraints excluded: chain B residue  685 GLU
Chi-restraints excluded: chain B residue  717 LYS
Chi-restraints excluded: chain B residue  744 ASN
Chi-restraints excluded: chain B residue  752 GLN
Chi-restraints excluded: chain B residue  810 LEU
Chi-restraints excluded: chain B residue  831 VAL
Chi-restraints excluded: chain B residue  833 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 100 optimal weight:    0.9980
   chunk 135 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 111 optimal weight:    1.9990
   chunk 117 optimal weight:    0.3980
   chunk 101 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 127 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 144 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 104 GLN
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.205826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.172735 restraints weight = 16572.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.177869 restraints weight = 9565.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.181346 restraints weight = 6589.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.183556 restraints weight = 5101.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.185287 restraints weight = 4285.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.4388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6814
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11764  Z= 0.147
  Angle     :  0.627  12.198  15912  Z= 0.301
  Chirality :  0.041   0.145   1876
  Planarity :  0.004   0.035   1990
  Dihedral  :  4.244  18.799   1580
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.91 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 33.47 %
    Favored  : 60.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.97 (0.21), residues: 1446
  helix:  0.06 (0.18), residues: 818
  sheet: -0.76 (0.41), residues: 142
  loop : -1.68 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 798 
 TYR   0.026   0.002   TYR A 283 
 PHE   0.016   0.001   PHE B 146 
 TRP   0.008   0.001   TRP A  95 
 HIS   0.006   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (11764)
  covalent geometry    : angle       0.62722 (15912)
  hydrogen bonds       : bond        0.03417 (  499)
  hydrogen bonds       : angle       4.60724 ( 1422)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 182
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 GLU cc_start: 0.7336 (tm-30) cc_final: 0.6797 (tt0)
REVERT: A  142 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7253 (t80)
REVERT: A  226 ARG cc_start: 0.7702 (ptp90) cc_final: 0.7405 (ptp90)
REVERT: A  231 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7283 (tt0)
REVERT: A  303 TYR cc_start: 0.6762 (OUTLIER) cc_final: 0.6157 (m-80)
REVERT: A  308 LYS cc_start: 0.7351 (ttmm) cc_final: 0.6940 (tttm)
REVERT: A  462 PRO cc_start: 0.7944 (Cg_endo) cc_final: 0.7670 (Cg_exo)
REVERT: A  487 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6224 (m-30)
REVERT: A  493 ILE cc_start: 0.8604 (mt) cc_final: 0.8379 (mt)
REVERT: A  640 LYS cc_start: 0.7901 (mmtm) cc_final: 0.7643 (mmtt)
REVERT: A  685 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7043 (mp0)
REVERT: B  142 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7677 (t80)
REVERT: B  332 GLU cc_start: 0.6836 (mt-10) cc_final: 0.6360 (tt0)
REVERT: B  463 ILE cc_start: 0.7430 (mm) cc_final: 0.7146 (mm)
REVERT: B  493 ILE cc_start: 0.8716 (mt) cc_final: 0.8406 (mt)
REVERT: B  508 LEU cc_start: 0.8479 (mm) cc_final: 0.8260 (mm)
REVERT: B  685 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.7012 (mp0)
REVERT: B  835 ASN cc_start: 0.7835 (m110) cc_final: 0.7472 (t0)
  outliers start: 70
  outliers final: 59
  residues processed: 230
  average time/residue: 0.1056
  time to fit residues: 35.6548
Evaluate side-chains
  241 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 176
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  220 MET
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  303 TYR
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  417 HIS
Chi-restraints excluded: chain A residue  422 PHE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  470 ASP
Chi-restraints excluded: chain A residue  487 ASP
Chi-restraints excluded: chain A residue  530 SER
Chi-restraints excluded: chain A residue  535 ILE
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  659 GLU
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  685 GLU
Chi-restraints excluded: chain A residue  717 LYS
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  745 ARG
Chi-restraints excluded: chain A residue  752 GLN
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain A residue  862 ILE
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  360 GLU
Chi-restraints excluded: chain B residue  361 PHE
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain B residue  422 PHE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  470 ASP
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  619 LEU
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain B residue  643 VAL
Chi-restraints excluded: chain B residue  659 GLU
Chi-restraints excluded: chain B residue  685 GLU
Chi-restraints excluded: chain B residue  724 VAL
Chi-restraints excluded: chain B residue  744 ASN
Chi-restraints excluded: chain B residue  752 GLN
Chi-restraints excluded: chain B residue  803 ASN
Chi-restraints excluded: chain B residue  810 LEU
Chi-restraints excluded: chain B residue  831 VAL
Chi-restraints excluded: chain B residue  833 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 134 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9990
   chunk 80 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 83 optimal weight:    0.6980
   chunk 120 optimal weight:    0.9980
   chunk 98 optimal weight:    4.9990
   chunk 135 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.205532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.172636 restraints weight = 16419.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.177742 restraints weight = 9529.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.181178 restraints weight = 6582.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.183501 restraints weight = 5105.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.185070 restraints weight = 4271.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.4364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6816
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11764  Z= 0.146
  Angle     :  0.644  13.376  15912  Z= 0.307
  Chirality :  0.042   0.147   1876
  Planarity :  0.004   0.035   1990
  Dihedral  :  4.281  19.747   1580
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.91 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 33.63 %
    Favored  : 60.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.91 (0.21), residues: 1446
  helix:  0.06 (0.18), residues: 818
  sheet: -0.19 (0.45), residues: 122
  loop : -1.71 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 668 
 TYR   0.025   0.002   TYR A 283 
 PHE   0.015   0.001   PHE B 146 
 TRP   0.008   0.001   TRP A 588 
 HIS   0.006   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (11764)
  covalent geometry    : angle       0.64440 (15912)
  hydrogen bonds       : bond        0.03376 (  499)
  hydrogen bonds       : angle       4.58041 ( 1422)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 174
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6826 (tt0)
REVERT: A  142 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7237 (t80)
REVERT: A  226 ARG cc_start: 0.7683 (ptp90) cc_final: 0.7364 (ptp90)
REVERT: A  231 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7308 (tt0)
REVERT: A  264 MET cc_start: 0.7084 (mpp) cc_final: 0.6781 (mpp)
REVERT: A  303 TYR cc_start: 0.6849 (OUTLIER) cc_final: 0.6222 (m-80)
REVERT: A  308 LYS cc_start: 0.7350 (ttmm) cc_final: 0.6924 (tttm)
REVERT: A  462 PRO cc_start: 0.7911 (Cg_endo) cc_final: 0.7646 (Cg_exo)
REVERT: A  487 ASP cc_start: 0.6756 (OUTLIER) cc_final: 0.6283 (m-30)
REVERT: A  493 ILE cc_start: 0.8634 (mt) cc_final: 0.8425 (mt)
REVERT: A  685 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7019 (mp0)
REVERT: B  142 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7623 (t80)
REVERT: B  332 GLU cc_start: 0.6754 (mt-10) cc_final: 0.6226 (tt0)
REVERT: B  493 ILE cc_start: 0.8717 (mt) cc_final: 0.8399 (mt)
REVERT: B  649 HIS cc_start: 0.7585 (OUTLIER) cc_final: 0.7054 (t70)
REVERT: B  685 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7074 (mp0)
REVERT: B  835 ASN cc_start: 0.7829 (m110) cc_final: 0.7451 (t0)
  outliers start: 70
  outliers final: 56
  residues processed: 222
  average time/residue: 0.1014
  time to fit residues: 33.6365
Evaluate side-chains
  234 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 171
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  303 TYR
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  422 PHE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  470 ASP
Chi-restraints excluded: chain A residue  487 ASP
Chi-restraints excluded: chain A residue  530 SER
Chi-restraints excluded: chain A residue  535 ILE
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  659 GLU
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  685 GLU
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  745 ARG
Chi-restraints excluded: chain A residue  752 GLN
Chi-restraints excluded: chain A residue  803 ASN
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  360 GLU
Chi-restraints excluded: chain B residue  361 PHE
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain B residue  422 PHE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  470 ASP
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  619 LEU
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain B residue  643 VAL
Chi-restraints excluded: chain B residue  649 HIS
Chi-restraints excluded: chain B residue  659 GLU
Chi-restraints excluded: chain B residue  664 ILE
Chi-restraints excluded: chain B residue  685 GLU
Chi-restraints excluded: chain B residue  724 VAL
Chi-restraints excluded: chain B residue  744 ASN
Chi-restraints excluded: chain B residue  752 GLN
Chi-restraints excluded: chain B residue  803 ASN
Chi-restraints excluded: chain B residue  810 LEU
Chi-restraints excluded: chain B residue  831 VAL
Chi-restraints excluded: chain B residue  833 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0970
   chunk 131 optimal weight:    0.6980
   chunk 127 optimal weight:    0.1980
   chunk 51 optimal weight:    0.9990
   chunk 109 optimal weight:    0.9990
   chunk 19 optimal weight:    0.3980
   chunk 75 optimal weight:    0.0980
   chunk 16 optimal weight:    0.8980
   chunk 20 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.2578

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 104 GLN
** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.208965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.176244 restraints weight = 16630.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.181581 restraints weight = 9510.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.185085 restraints weight = 6486.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.187485 restraints weight = 4996.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.189108 restraints weight = 4162.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.4408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6742
moved from start:          0.3106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11764  Z= 0.109
  Angle     :  0.619  13.604  15912  Z= 0.295
  Chirality :  0.040   0.140   1876
  Planarity :  0.004   0.036   1990
  Dihedral  :  4.105  19.677   1580
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.01 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 34.98 %
    Favored  : 60.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.73 (0.22), residues: 1446
  helix:  0.23 (0.18), residues: 818
  sheet: -0.05 (0.45), residues: 122
  loop : -1.69 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 798 
 TYR   0.020   0.001   TYR A 283 
 PHE   0.014   0.001   PHE B 146 
 TRP   0.009   0.001   TRP A  95 
 HIS   0.007   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (11764)
  covalent geometry    : angle       0.61872 (15912)
  hydrogen bonds       : bond        0.03015 (  499)
  hydrogen bonds       : angle       4.41259 ( 1422)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 175
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6171 (mt-10)
REVERT: A  142 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.7370 (t80)
REVERT: A  226 ARG cc_start: 0.7624 (ptp90) cc_final: 0.7307 (ptp90)
REVERT: A  303 TYR cc_start: 0.6906 (OUTLIER) cc_final: 0.6299 (m-80)
REVERT: A  308 LYS cc_start: 0.7329 (ttmm) cc_final: 0.6927 (tttm)
REVERT: A  462 PRO cc_start: 0.7870 (Cg_endo) cc_final: 0.7593 (Cg_exo)
REVERT: A  487 ASP cc_start: 0.6615 (OUTLIER) cc_final: 0.6113 (m-30)
REVERT: A  685 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7010 (mp0)
REVERT: B  142 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7667 (t80)
REVERT: B  332 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6228 (tt0)
REVERT: B  462 PRO cc_start: 0.7912 (Cg_endo) cc_final: 0.7661 (Cg_exo)
REVERT: B  493 ILE cc_start: 0.8690 (mt) cc_final: 0.8410 (mt)
REVERT: B  685 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7118 (mp0)
REVERT: B  835 ASN cc_start: 0.7798 (m110) cc_final: 0.7435 (t0)
  outliers start: 53
  outliers final: 44
  residues processed: 213
  average time/residue: 0.1009
  time to fit residues: 31.9355
Evaluate side-chains
  221 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 171
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  303 TYR
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  417 HIS
Chi-restraints excluded: chain A residue  422 PHE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  470 ASP
Chi-restraints excluded: chain A residue  487 ASP
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  659 GLU
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  685 GLU
Chi-restraints excluded: chain A residue  717 LYS
Chi-restraints excluded: chain A residue  745 ARG
Chi-restraints excluded: chain A residue  752 GLN
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  360 GLU
Chi-restraints excluded: chain B residue  361 PHE
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain B residue  422 PHE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  470 ASP
Chi-restraints excluded: chain B residue  487 ASP
Chi-restraints excluded: chain B residue  530 SER
Chi-restraints excluded: chain B residue  619 LEU
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain B residue  659 GLU
Chi-restraints excluded: chain B residue  664 ILE
Chi-restraints excluded: chain B residue  685 GLU
Chi-restraints excluded: chain B residue  744 ASN
Chi-restraints excluded: chain B residue  752 GLN
Chi-restraints excluded: chain B residue  810 LEU
Chi-restraints excluded: chain B residue  831 VAL
Chi-restraints excluded: chain B residue  833 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 136 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 141 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 82 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9980
   chunk 144 optimal weight:    0.9990
   chunk 127 optimal weight:    0.1980
   chunk 30 optimal weight:    1.9990
   chunk 126 optimal weight:    0.4980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.206131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.173143 restraints weight = 16692.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.178367 restraints weight = 9609.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.181893 restraints weight = 6601.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.184227 restraints weight = 5084.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.185752 restraints weight = 4257.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.4395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6807
moved from start:          0.3116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11764  Z= 0.139
  Angle     :  0.624  10.063  15912  Z= 0.298
  Chirality :  0.041   0.135   1876
  Planarity :  0.004   0.035   1990
  Dihedral  :  4.171  18.676   1580
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.70 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 34.58 %
    Favored  : 60.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.79 (0.21), residues: 1446
  helix:  0.18 (0.18), residues: 818
  sheet: -0.15 (0.45), residues: 122
  loop : -1.70 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 798 
 TYR   0.022   0.002   TYR A 283 
 PHE   0.015   0.001   PHE B 146 
 TRP   0.007   0.001   TRP A 588 
 HIS   0.006   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (11764)
  covalent geometry    : angle       0.62445 (15912)
  hydrogen bonds       : bond        0.03219 (  499)
  hydrogen bonds       : angle       4.45815 ( 1422)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2196.38 seconds
wall clock time: 38 minutes 43.73 seconds (2323.73 seconds total)