Starting phenix.real_space_refine
on Wed Mar  4 09:19:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qq6_4619/03_2026/6qq6_4619.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qq6_4619/03_2026/6qq6_4619.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qq6_4619/03_2026/6qq6_4619.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qq6_4619/03_2026/6qq6_4619.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qq6_4619/03_2026/6qq6_4619.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qq6_4619/03_2026/6qq6_4619.cif"
  }
  resolution = 3.3
  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=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Fe      6      7.16       5
     P       3      5.49       5
     S      46      5.16       5
     C    8019      2.51       5
     N    1991      2.21       5
     O    2056      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12123
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5872
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 743, 5862
          Classifications: {'peptide': 743}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 35, 'TRANS': 707}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
      Conformer: "B"
        Number of residues, atoms: 743, 5862
          Classifications: {'peptide': 743}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 35, 'TRANS': 707}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
          bond proxies already assigned to first conformer: 6041
    Chain: "B"
      Number of atoms: 5872
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 743, 5862
          Classifications: {'peptide': 743}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 35, 'TRANS': 707}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
      Conformer: "B"
        Number of residues, atoms: 743, 5862
          Classifications: {'peptide': 743}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 35, 'TRANS': 707}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
          bond proxies already assigned to first conformer: 6041
    Chain: "A"
      Number of atoms: 130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 130
          Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2, 'LOP': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "B"
      Number of atoms: 231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 231
          Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2, 'LMT': 2, 'LOP': 2}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 17
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 9
          Classifications: {'water': 9}
          Link IDs: {None: 8}
    Chain: "B"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 9
          Classifications: {'water': 9}
          Link IDs: {None: 8}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AHIS A 224 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 224 " occ=0.50
    residue:
      pdb=" N  AHIS B 224 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS B 224 " occ=0.50
  Time building chain proxies: 4.93, per 1000 atoms: 0.41
  Number of scatterers: 12123
  At special positions: 0
  Unit cell: (118.65, 74.55, 103.95, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Fe      6     26.01
     Ca      2     19.99
     S      46     16.00
     P       3     15.00
     O    2056      8.00
     N    1991      7.00
     C    8019      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.20
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2688

  Finding SS restraints...
    Secondary structure from input PDB file:
      79 helices and 3 sheets defined
      67.9% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 32
      removed outlier: 3.559A  pdb=" N   PHE A   9 " --> pdb=" O   ARG A   5 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   TYR A  25 " --> pdb=" O   LEU A  21 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLU A  28 " --> pdb=" O   PHE A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 64
    Processing helix  chain 'A' and resid 65 through 69
      removed outlier: 3.588A  pdb=" N   LEU A  69 " --> pdb=" O   GLY A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 105
      removed outlier: 3.883A  pdb=" N   LEU A  88 " --> pdb=" O   THR A  84 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ASP A 102 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ALA A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 127
      removed outlier: 4.155A  pdb=" N   ALA A 125 " --> pdb=" O   GLU A 121 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLU A 126 " --> pdb=" O   GLN A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 160
      removed outlier: 3.988A  pdb=" N   ALA A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   TYR A 155 " --> pdb=" O   GLN A 151 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   TYR A 156 " --> pdb=" O   THR A 152 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   PHE A 160 " --> pdb=" O   TYR A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 200
      removed outlier: 3.977A  pdb=" N   HIS A 191 " --> pdb=" O   ARG A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 254
      removed outlier: 3.722A  pdb=" N   LEU A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 281
    Processing helix  chain 'A' and resid 282 through 304
      removed outlier: 3.762A  pdb=" N   VAL A 290 " --> pdb=" O   LEU A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 309
      removed outlier: 3.566A  pdb=" N   VAL A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 355
      removed outlier: 3.880A  pdb=" N   ALA A 335 " --> pdb=" O   HIS A 331 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   PHE A 343 " --> pdb=" O   ILE A 339 " (cutoff:3.500A)
      Proline residue:  A 352  - end of helix
      removed outlier: 3.804A  pdb=" N   ASN A 355 " --> pdb=" O   ALA A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 390
    Processing helix  chain 'A' and resid 394 through 398
      removed outlier: 3.683A  pdb=" N   ASN A 398 " --> pdb=" O   PRO A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 435
      removed outlier: 3.924A  pdb=" N   GLY A 433 " --> pdb=" O   LEU A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 438
      No H-bonds generated for 'chain 'A' and resid 436 through 438'
    Processing helix  chain 'A' and resid 447 through 461
    Processing helix  chain 'A' and resid 462 through 466
    Processing helix  chain 'A' and resid 475 through 479
    Processing helix  chain 'A' and resid 490 through 498
      removed outlier: 3.967A  pdb=" N   GLU A 494 " --> pdb=" O   GLU A 490 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA A 495 " --> pdb=" O   GLY A 491 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   PHE A 496 " --> pdb=" O   PHE A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 508
    Processing helix  chain 'A' and resid 517 through 522
    Processing helix  chain 'A' and resid 523 through 525
      No H-bonds generated for 'chain 'A' and resid 523 through 525'
    Processing helix  chain 'A' and resid 526 through 531
      removed outlier: 4.066A  pdb=" N   GLY A 530 " --> pdb=" O   LEU A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 538
      removed outlier: 3.897A  pdb=" N   THR A 535 " --> pdb=" O   ILE A 532 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   PHE A 536 " --> pdb=" O   PRO A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 558
      removed outlier: 3.647A  pdb=" N   MET A 549 " --> pdb=" O   THR A 545 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   SER A 554 " --> pdb=" O   ALA A 550 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   SER A 556 " --> pdb=" O   GLY A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 578
      removed outlier: 3.590A  pdb=" N   LEU A 576 " --> pdb=" O   GLU A 572 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   LYS A 577 " --> pdb=" O   ASN A 573 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   THR A 578 " --> pdb=" O   TRP A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 585
      removed outlier: 7.108A  pdb=" N   TRP A 582 " --> pdb=" O   ARG A 579 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   GLU A 584 " --> pdb=" O   PRO A 581 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ASN A 585 " --> pdb=" O   TRP A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 586 through 602
      removed outlier: 3.579A  pdb=" N   VAL A 594 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ALA A 597 " --> pdb=" O   PHE A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 610
    Processing helix  chain 'A' and resid 616 through 620
    Processing helix  chain 'A' and resid 625 through 635
      removed outlier: 3.542A  pdb=" N   HIS A 629 " --> pdb=" O   THR A 625 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   PHE A 635 " --> pdb=" O   HIS A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 651
      removed outlier: 3.584A  pdb=" N   LEU A 647 " --> pdb=" O   LEU A 643 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ARG A 651 " --> pdb=" O   LEU A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 670
    Processing helix  chain 'A' and resid 670 through 681
      removed outlier: 3.582A  pdb=" N   ILE A 679 " --> pdb=" O   LEU A 675 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   PHE A 680 " --> pdb=" O   ALA A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 697
      removed outlier: 3.608A  pdb=" N   ILE A 686 " --> pdb=" O   SER A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 698 through 704
      removed outlier: 3.740A  pdb=" N   ARG A 703 " --> pdb=" O   MET A 699 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 704 through 709
      removed outlier: 3.506A  pdb=" N   GLN A 709 " --> pdb=" O   GLU A 705 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 719
      removed outlier: 3.574A  pdb=" N   ARG A 717 " --> pdb=" O   LEU A 713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 720 through 742
      removed outlier: 4.729A  pdb=" N   VAL A 726 " --> pdb=" O   PHE A 722 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 32
      removed outlier: 3.551A  pdb=" N   PHE B   9 " --> pdb=" O   ARG B   5 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   TYR B  25 " --> pdb=" O   LEU B  21 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLU B  28 " --> pdb=" O   PHE B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 64
    Processing helix  chain 'B' and resid 65 through 69
      removed outlier: 3.581A  pdb=" N   LEU B  69 " --> pdb=" O   GLY B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 105
      removed outlier: 3.826A  pdb=" N   LEU B  88 " --> pdb=" O   THR B  84 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   ASP B 102 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ALA B 103 " --> pdb=" O   ALA B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 127
      removed outlier: 4.164A  pdb=" N   ALA B 125 " --> pdb=" O   GLU B 121 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLU B 126 " --> pdb=" O   GLN B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 160
      removed outlier: 3.967A  pdb=" N   ALA B 154 " --> pdb=" O   ALA B 150 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   TYR B 155 " --> pdb=" O   GLN B 151 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   TYR B 156 " --> pdb=" O   THR B 152 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   PHE B 160 " --> pdb=" O   TYR B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 200
      removed outlier: 3.976A  pdb=" N   HIS B 191 " --> pdb=" O   ARG B 187 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ALA B 200 " --> pdb=" O   THR B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 254
      removed outlier: 3.733A  pdb=" N   LEU B 246 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 281
    Processing helix  chain 'B' and resid 282 through 304
      removed outlier: 3.761A  pdb=" N   VAL B 290 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 309
      removed outlier: 3.553A  pdb=" N   VAL B 308 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 355
      removed outlier: 3.881A  pdb=" N   ALA B 335 " --> pdb=" O   HIS B 331 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE B 343 " --> pdb=" O   ILE B 339 " (cutoff:3.500A)
      Proline residue:  B 352  - end of helix
      removed outlier: 3.806A  pdb=" N   ASN B 355 " --> pdb=" O   ALA B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 363 through 390
    Processing helix  chain 'B' and resid 394 through 398
      removed outlier: 3.695A  pdb=" N   ASN B 398 " --> pdb=" O   PRO B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 435
      removed outlier: 3.928A  pdb=" N   GLY B 433 " --> pdb=" O   LEU B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 438
      No H-bonds generated for 'chain 'B' and resid 436 through 438'
    Processing helix  chain 'B' and resid 447 through 461
    Processing helix  chain 'B' and resid 462 through 466
    Processing helix  chain 'B' and resid 475 through 479
    Processing helix  chain 'B' and resid 493 through 498
    Processing helix  chain 'B' and resid 498 through 508
    Processing helix  chain 'B' and resid 517 through 522
    Processing helix  chain 'B' and resid 526 through 531
      removed outlier: 4.065A  pdb=" N   GLY B 530 " --> pdb=" O   LEU B 526 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 532 through 538
      removed outlier: 3.899A  pdb=" N   THR B 535 " --> pdb=" O   ILE B 532 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   PHE B 536 " --> pdb=" O   PRO B 533 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 545 through 558
      removed outlier: 3.644A  pdb=" N   MET B 549 " --> pdb=" O   THR B 545 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   SER B 556 " --> pdb=" O   GLY B 552 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 571 through 576
      removed outlier: 4.057A  pdb=" N   LEU B 576 " --> pdb=" O   GLU B 572 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 577 through 579
      No H-bonds generated for 'chain 'B' and resid 577 through 579'
    Processing helix  chain 'B' and resid 580 through 585
      removed outlier: 3.932A  pdb=" N   GLU B 584 " --> pdb=" O   PRO B 581 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ASN B 585 " --> pdb=" O   TRP B 582 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 586 through 603
      removed outlier: 3.516A  pdb=" N   VAL B 594 " --> pdb=" O   LEU B 590 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA B 597 " --> pdb=" O   PHE B 593 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 605 through 610
    Processing helix  chain 'B' and resid 616 through 620
    Processing helix  chain 'B' and resid 625 through 635
      removed outlier: 3.547A  pdb=" N   HIS B 629 " --> pdb=" O   THR B 625 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   PHE B 635 " --> pdb=" O   HIS B 631 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 643 through 651
      removed outlier: 3.589A  pdb=" N   LEU B 647 " --> pdb=" O   LEU B 643 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   VAL B 649 " --> pdb=" O   PHE B 645 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ARG B 651 " --> pdb=" O   LEU B 647 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 663 through 681
      removed outlier: 3.940A  pdb=" N   LEU B 671 " --> pdb=" O   ALA B 667 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LEU B 673 " --> pdb=" O   TRP B 669 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ILE B 679 " --> pdb=" O   LEU B 675 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   PHE B 680 " --> pdb=" O   ALA B 676 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 682 through 697
      removed outlier: 3.599A  pdb=" N   ILE B 686 " --> pdb=" O   SER B 682 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 698 through 704
      removed outlier: 3.515A  pdb=" N   ALA B 702 " --> pdb=" O   GLY B 698 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ARG B 703 " --> pdb=" O   MET B 699 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 704 through 709
      removed outlier: 3.550A  pdb=" N   GLN B 709 " --> pdb=" O   GLU B 705 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 712 through 719
      removed outlier: 3.627A  pdb=" N   ARG B 717 " --> pdb=" O   LEU B 713 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 720 through 742
      removed outlier: 4.669A  pdb=" N   VAL B 726 " --> pdb=" O   PHE B 722 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41
      removed outlier: 4.018A  pdb=" N   PHE A  49 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 41
      removed outlier: 4.015A  pdb=" N   PHE B  49 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72

    611 hydrogen bonds defined for protein.
    1764 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.99

  Time building geometry restraints manager: 1.55 seconds

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

  Histogram of bond lengths:
        1.18 -     1.35: 3747
        1.35 -     1.53: 7671
        1.53 -     1.70: 992
        1.70 -     1.88: 88
        1.88 -     2.05: 16
  Bond restraints: 12514
  Sorted by residual:
  bond pdb=" C1B LMT B 807 "
       pdb=" O5B LMT B 807 "
    ideal  model  delta    sigma   weight residual
    1.393  1.508 -0.115 2.00e-02 2.50e+03 3.33e+01
  bond pdb=" C1B LMT B 808 "
       pdb=" O5B LMT B 808 "
    ideal  model  delta    sigma   weight residual
    1.393  1.506 -0.113 2.00e-02 2.50e+03 3.20e+01
  bond pdb=" C1' LMT B 807 "
       pdb=" O5' LMT B 807 "
    ideal  model  delta    sigma   weight residual
    1.408  1.499 -0.091 2.00e-02 2.50e+03 2.07e+01
  bond pdb=" C1' LMT B 808 "
       pdb=" O5' LMT B 808 "
    ideal  model  delta    sigma   weight residual
    1.408  1.493 -0.085 2.00e-02 2.50e+03 1.79e+01
  bond pdb=" C24 LOP B 806 "
       pdb=" O6  LOP B 806 "
    ideal  model  delta    sigma   weight residual
    1.325  1.401 -0.076 2.00e-02 2.50e+03 1.45e+01
  ... (remaining 12509 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 16369
        2.27 -     4.55: 552
        4.55 -     6.82: 134
        6.82 -     9.10: 39
        9.10 -    11.37: 15
  Bond angle restraints: 17109
  Sorted by residual:
  angle pdb=" N   ILE B 712 "
        pdb=" CA  ILE B 712 "
        pdb=" C   ILE B 712 "
      ideal   model   delta    sigma   weight residual
     112.96  106.66    6.30 1.00e+00 1.00e+00 3.97e+01
  angle pdb=" N   ILE A 712 "
        pdb=" CA  ILE A 712 "
        pdb=" C   ILE A 712 "
      ideal   model   delta    sigma   weight residual
     112.96  106.69    6.27 1.00e+00 1.00e+00 3.93e+01
  angle pdb=" N   GLU A 572 "
        pdb=" CA  GLU A 572 "
        pdb=" C   GLU A 572 "
      ideal   model   delta    sigma   weight residual
     111.14  104.83    6.31 1.08e+00 8.57e-01 3.41e+01
  angle pdb=" CA  PHE A 536 "
        pdb=" C   PHE A 536 "
        pdb=" N   HIS A 537 "
      ideal   model   delta    sigma   weight residual
     118.59  127.92   -9.33 1.63e+00 3.76e-01 3.28e+01
  angle pdb=" N   ARG B 579 "
        pdb=" CA  ARG B 579 "
        pdb=" C   ARG B 579 "
      ideal   model   delta    sigma   weight residual
     111.36  117.57   -6.21 1.09e+00 8.42e-01 3.25e+01
  ... (remaining 17104 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.36: 6525
       22.36 -    44.71: 442
       44.71 -    67.07: 81
       67.07 -    89.43: 16
       89.43 -   111.79: 14
  Dihedral angle restraints: 7078
    sinusoidal: 2846
      harmonic: 4232
  Sorted by residual:
  dihedral pdb=" CA  ASN A 214 "
           pdb=" C   ASN A 214 "
           pdb=" N   TRP A 215 "
           pdb=" CA  TRP A 215 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.43  -25.57     0      5.00e+00 4.00e-02 2.61e+01
  dihedral pdb=" CA  ASN B 214 "
           pdb=" C   ASN B 214 "
           pdb=" N   TRP B 215 "
           pdb=" CA  TRP B 215 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.51  -25.49     0      5.00e+00 4.00e-02 2.60e+01
  dihedral pdb=" CA  TYR B 652 "
           pdb=" C   TYR B 652 "
           pdb=" N   ILE B 653 "
           pdb=" CA  ILE B 653 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.52   23.48     0      5.00e+00 4.00e-02 2.20e+01
  ... (remaining 7075 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1510
       0.066 -    0.133: 256
       0.133 -    0.199: 31
       0.199 -    0.266: 5
       0.266 -    0.332: 5
  Chirality restraints: 1807
  Sorted by residual:
  chirality pdb=" CA  ILE B 392 "
            pdb=" N   ILE B 392 "
            pdb=" C   ILE B 392 "
            pdb=" CB  ILE B 392 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.77   -0.33 2.00e-01 2.50e+01 2.76e+00
  chirality pdb=" CB  ILE A 620 "
            pdb=" CA  ILE A 620 "
            pdb=" CG1 ILE A 620 "
            pdb=" CG2 ILE A 620 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.31 2.00e-01 2.50e+01 2.38e+00
  chirality pdb=" CB  ILE B 620 "
            pdb=" CA  ILE B 620 "
            pdb=" CG1 ILE B 620 "
            pdb=" CG2 ILE B 620 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.30 2.00e-01 2.50e+01 2.21e+00
  ... (remaining 1804 not shown)

  Planarity restraints: 2113
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 179 "    0.012 2.00e-02 2.50e+03   2.41e-02 5.82e+00
        pdb=" C   THR A 179 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   THR A 179 "    0.016 2.00e-02 2.50e+03
        pdb=" N   LEU A 180 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B 588 "   -0.039 5.00e-02 4.00e+02   5.87e-02 5.52e+00
        pdb=" N   PRO B 589 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO B 589 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 589 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 588 "   -0.038 5.00e-02 4.00e+02   5.68e-02 5.15e+00
        pdb=" N   PRO A 589 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO A 589 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 589 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 2110 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.52: 89
        2.52 -     3.11: 8141
        3.11 -     3.71: 19849
        3.71 -     4.30: 28771
        4.30 -     4.90: 48210
  Nonbonded interactions: 105060
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 162 "
            pdb=" OD1 ASP A 162 "
     model   vdw
     1.924 3.040
  nonbonded pdb=" NE2 HIS B 538 "
            pdb="FE    FE B 803 "
     model   vdw
     1.988 2.340
  nonbonded pdb=" NE2 HIS A 538 "
            pdb="FE    FE A 803 "
     model   vdw
     1.989 2.340
  nonbonded pdb=" NE2 HIS B 631 "
            pdb="FE   HEM B 801 "
     model   vdw
     1.996 3.080
  nonbonded pdb=" NE2 HIS A 631 "
            pdb="FE   HEM A 801 "
     model   vdw
     1.996 3.080
  ... (remaining 105055 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 223 or resid 225 through 804 or (resid 805 and ( \ 
name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15  \ 
or name C16 or name C17 or name C18 or name C19 or name C2 or name C20 or name C \ 
24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or nam \ 
e C30 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name  \ 
N1 or name O1 or name O2 or name O3 or name O4 or name O5 or name O6 or name O7  \ 
or name O8 or name P1 ))))
  selection = (chain 'B' and (resid 1 through 223 or resid 225 through 804 or (resid 805 and ( \ 
name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15  \ 
or name C16 or name C17 or name C18 or name C19 or name C2 or name C20 or name C \ 
24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or nam \ 
e C30 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name  \ 
N1 or name O1 or name O2 or name O3 or name O4 or name O5 or name O6 or name O7  \ 
or name O8 or name P1 ))))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     15.760
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.040
  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:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.270  12518  Z= 0.304
  Angle     :  1.076  11.372  17109  Z= 0.544
  Chirality :  0.055   0.332   1807
  Planarity :  0.007   0.059   2113
  Dihedral  : 16.787 111.787   4390
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.08 (0.15), residues: 1488
  helix: -3.17 (0.11), residues: 988
  sheet:  None (None), residues: 0
  loop : -3.43 (0.21), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 328 
 TYR   0.019   0.002   TYR A 468 
 PHE   0.022   0.002   PHE A 635 
 TRP   0.024   0.002   TRP A 215 
 HIS   0.007   0.002   HIS B 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00657 (12514)
  covalent geometry    : angle       1.07581 (17109)
  hydrogen bonds       : bond        0.15790 (  611)
  hydrogen bonds       : angle       6.99370 ( 1764)
  Misc. bond           : bond        0.25504 (    4)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.3616 (ptp) cc_final: 0.2965 (ttp)
REVERT: A  718 TRP cc_start: 0.6828 (t60) cc_final: 0.6101 (t60)
REVERT: B    1 MET cc_start: 0.3558 (ptp) cc_final: 0.3098 (ptp)
REVERT: B  355 ASN cc_start: 0.8773 (t0) cc_final: 0.8304 (t0)
REVERT: B  430 MET cc_start: 0.8193 (mmm) cc_final: 0.7889 (tpt)
REVERT: B  718 TRP cc_start: 0.6139 (t60) cc_final: 0.5721 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 218
  average time/residue: 0.1221
  time to fit residues: 38.1408
Evaluate side-chains
  159 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
A 130 ASN
A 224 HIS    A
A 355 ASN
A 398 ASN
B  68 GLN
B 130 ASN
B 214 ASN
B 355 ASN
B 398 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.131258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.096091 restraints weight = 27848.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.2992 rms_B_bonded: 2.49
r_work: 0.2841 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2832
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2832
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.227  12518  Z= 0.139
  Angle     :  0.664   9.002  17109  Z= 0.326
  Chirality :  0.042   0.335   1807
  Planarity :  0.005   0.052   2113
  Dihedral  : 11.736  85.691   1874
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  8.93 %
    Favored  : 90.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.83 (0.20), residues: 1488
  helix: -1.39 (0.15), residues: 1000
  sheet:  None (None), residues: 0
  loop : -2.68 (0.25), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 432 
 TYR   0.020   0.002   TYR B 108 
 PHE   0.014   0.001   PHE B 635 
 TRP   0.021   0.001   TRP B 215 
 HIS   0.005   0.001   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (12514)
  covalent geometry    : angle       0.66448 (17109)
  hydrogen bonds       : bond        0.03725 (  611)
  hydrogen bonds       : angle       4.67974 ( 1764)
  Misc. bond           : bond        0.17996 (    4)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 175
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.3391 (ptp) cc_final: 0.2756 (ttp)
REVERT: A  231 MET cc_start: 0.7683 (mmm) cc_final: 0.7183 (ttt)
REVERT: A  280 ARG cc_start: 0.7463 (mtm110) cc_final: 0.6945 (mtm110)
REVERT: A  445 LYS cc_start: 0.6266 (ptmt) cc_final: 0.6056 (ptmt)
REVERT: A  494 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7765 (tm-30)
REVERT: A  708 MET cc_start: 0.8622 (mmt) cc_final: 0.8364 (tpt)
REVERT: A  718 TRP cc_start: 0.7405 (t60) cc_final: 0.6499 (t60)
REVERT: B    1 MET cc_start: 0.3154 (ptp) cc_final: 0.2622 (ptp)
REVERT: B  231 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7233 (ttp)
REVERT: B  355 ASN cc_start: 0.9064 (t0) cc_final: 0.8523 (t0)
REVERT: B  430 MET cc_start: 0.8586 (mmm) cc_final: 0.8186 (tpt)
REVERT: B  652 TYR cc_start: 0.8145 (m-80) cc_final: 0.7899 (m-80)
REVERT: B  718 TRP cc_start: 0.6938 (t60) cc_final: 0.6268 (t60)
  outliers start: 12
  outliers final: 3
  residues processed: 179
  average time/residue: 0.1069
  time to fit residues: 28.1987
Evaluate side-chains
  156 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 152
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  561 VAL
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  435 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 78 optimal weight:   10.0000
   chunk 60 optimal weight:    0.0370
   chunk 41 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 137 optimal weight:    0.8980
   chunk 83 optimal weight:    0.8980
   chunk 122 optimal weight:    0.6980
   chunk 20 optimal weight:    6.9990
   chunk 146 optimal weight:    0.9990
   chunk 7 optimal weight:    0.2980
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
A 305 HIS
A 355 ASN
B  68 GLN
** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 631 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.132422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.099314 restraints weight = 36562.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 2.94
r_work: 0.2825 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2816
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2816 r_free = 0.2816    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2816 r_free = 0.2816    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2816
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.209  12518  Z= 0.120
  Angle     :  0.619   8.554  17109  Z= 0.302
  Chirality :  0.040   0.242   1807
  Planarity :  0.004   0.062   2113
  Dihedral  : 10.141  86.284   1874
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 11.17 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.88 (0.21), residues: 1488
  helix: -0.67 (0.16), residues: 1000
  sheet:  None (None), residues: 0
  loop : -2.29 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 358 
 TYR   0.016   0.001   TYR B 108 
 PHE   0.012   0.001   PHE B 691 
 TRP   0.022   0.001   TRP B 215 
 HIS   0.004   0.001   HIS B 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (12514)
  covalent geometry    : angle       0.61949 (17109)
  hydrogen bonds       : bond        0.03416 (  611)
  hydrogen bonds       : angle       4.39253 ( 1764)
  Misc. bond           : bond        0.17291 (    4)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 161
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.3266 (ptp) cc_final: 0.2596 (ttp)
REVERT: A   39 GLU cc_start: 0.6735 (mm-30) cc_final: 0.6396 (mm-30)
REVERT: A  280 ARG cc_start: 0.7646 (mtm110) cc_final: 0.7036 (mtm110)
REVERT: A  320 GLN cc_start: 0.8201 (pt0) cc_final: 0.7753 (mp10)
REVERT: A  494 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8018 (tm-30)
REVERT: A  701 TYR cc_start: 0.8924 (t80) cc_final: 0.8706 (t80)
REVERT: A  718 TRP cc_start: 0.7443 (t60) cc_final: 0.6510 (t60)
REVERT: B    1 MET cc_start: 0.3197 (ptp) cc_final: 0.2761 (ptp)
REVERT: B  355 ASN cc_start: 0.9125 (t0) cc_final: 0.8664 (t0)
REVERT: B  430 MET cc_start: 0.8580 (mmm) cc_final: 0.8216 (tpt)
REVERT: B  591 MET cc_start: 0.8562 (mtp) cc_final: 0.8309 (ttm)
REVERT: B  652 TYR cc_start: 0.8139 (m-80) cc_final: 0.7870 (m-80)
REVERT: B  718 TRP cc_start: 0.7012 (t60) cc_final: 0.6301 (t60)
  outliers start: 10
  outliers final: 7
  residues processed: 166
  average time/residue: 0.1113
  time to fit residues: 27.1414
Evaluate side-chains
  156 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 149
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  302 PHE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  355 ASN
Chi-restraints excluded: chain A residue  561 VAL
Chi-restraints excluded: chain B residue  435 VAL
Chi-restraints excluded: chain B residue  646 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 147 optimal weight:    0.9990
   chunk 113 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 138 optimal weight:    4.9990
   chunk 135 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 92 optimal weight:    4.9990
   chunk 141 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   chunk 124 optimal weight:    4.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B  68 GLN
B 214 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.135552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.100386 restraints weight = 35263.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 2.80
r_work: 0.2828 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2818
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2818 r_free = 0.2818    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2818 r_free = 0.2818    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2818
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.205  12518  Z= 0.133
  Angle     :  0.622  10.314  17109  Z= 0.302
  Chirality :  0.041   0.283   1807
  Planarity :  0.004   0.052   2113
  Dihedral  :  9.628  83.628   1874
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.68 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.22), residues: 1488
  helix: -0.33 (0.17), residues: 1006
  sheet:  None (None), residues: 0
  loop : -2.00 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 432 
 TYR   0.033   0.002   TYR B 406 
 PHE   0.013   0.001   PHE B 194 
 TRP   0.020   0.001   TRP B 215 
 HIS   0.004   0.001   HIS B 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (12514)
  covalent geometry    : angle       0.62211 (17109)
  hydrogen bonds       : bond        0.03373 (  611)
  hydrogen bonds       : angle       4.18788 ( 1764)
  Misc. bond           : bond        0.15990 (    4)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 156
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3391 (ptp) cc_final: 0.2683 (ttp)
REVERT: A   67 MET cc_start: 0.8749 (mtt) cc_final: 0.8486 (mtt)
REVERT: A  280 ARG cc_start: 0.7689 (mtm110) cc_final: 0.7129 (mtm110)
REVERT: A  320 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7854 (mp10)
REVERT: A  445 LYS cc_start: 0.6199 (ptmt) cc_final: 0.4891 (mmtm)
REVERT: A  494 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8165 (tm-30)
REVERT: A  708 MET cc_start: 0.8423 (mmt) cc_final: 0.7996 (tpt)
REVERT: A  718 TRP cc_start: 0.7458 (t60) cc_final: 0.6544 (t60)
REVERT: B    1 MET cc_start: 0.3211 (ptp) cc_final: 0.2663 (ptp)
REVERT: B  355 ASN cc_start: 0.9160 (t0) cc_final: 0.8731 (t0)
REVERT: B  401 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7808 (pp)
REVERT: B  515 MET cc_start: 0.7907 (mmp) cc_final: 0.6846 (mtm)
REVERT: B  591 MET cc_start: 0.8565 (mtp) cc_final: 0.8302 (mtt)
REVERT: B  601 MET cc_start: 0.8960 (ttp) cc_final: 0.8721 (tmm)
REVERT: B  652 TYR cc_start: 0.8187 (m-80) cc_final: 0.7954 (m-80)
REVERT: B  718 TRP cc_start: 0.7016 (t60) cc_final: 0.6320 (t60)
  outliers start: 15
  outliers final: 9
  residues processed: 164
  average time/residue: 0.1142
  time to fit residues: 27.4094
Evaluate side-chains
  161 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 150
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  320 GLN
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  561 VAL
Chi-restraints excluded: chain A residue  601 MET
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  435 VAL
Chi-restraints excluded: chain B residue  708 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 95 optimal weight:    0.8980
   chunk 114 optimal weight:    0.7980
   chunk 147 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9980
   chunk 107 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 137 optimal weight:    0.5980
   chunk 67 optimal weight:    0.5980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 473 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 = 0.3488 r_free = 0.3488 target = 0.134327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.097753 restraints weight = 35161.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 3.10
r_work: 0.2830 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2818
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2818 r_free = 0.2818    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2818 r_free = 0.2818    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2818
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.155  12518  Z= 0.120
  Angle     :  0.605  10.349  17109  Z= 0.292
  Chirality :  0.040   0.192   1807
  Planarity :  0.004   0.042   2113
  Dihedral  :  9.033  79.683   1874
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 13.23 %
    Favored  : 85.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.22), residues: 1488
  helix:  0.07 (0.17), residues: 980
  sheet:  None (None), residues: 0
  loop : -1.88 (0.29), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 432 
 TYR   0.014   0.001   TYR B 468 
 PHE   0.010   0.001   PHE A 461 
 TRP   0.020   0.001   TRP A 215 
 HIS   0.004   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (12514)
  covalent geometry    : angle       0.60467 (17109)
  hydrogen bonds       : bond        0.03254 (  611)
  hydrogen bonds       : angle       4.10066 ( 1764)
  Misc. bond           : bond        0.14062 (    4)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 156
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3381 (ptp) cc_final: 0.2540 (ttp)
REVERT: A   67 MET cc_start: 0.8817 (mtt) cc_final: 0.8572 (mtt)
REVERT: A  280 ARG cc_start: 0.7731 (mtm110) cc_final: 0.7143 (mtm110)
REVERT: A  320 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7816 (mp10)
REVERT: A  445 LYS cc_start: 0.6126 (ptmt) cc_final: 0.4857 (mmtm)
REVERT: A  494 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8169 (tm-30)
REVERT: A  601 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8333 (tmm)
REVERT: A  657 TYR cc_start: 0.7479 (t80) cc_final: 0.7132 (t80)
REVERT: A  718 TRP cc_start: 0.7482 (t60) cc_final: 0.6585 (t60)
REVERT: B    1 MET cc_start: 0.3042 (ptp) cc_final: 0.2521 (ptp)
REVERT: B  355 ASN cc_start: 0.9137 (t0) cc_final: 0.8718 (t0)
REVERT: B  515 MET cc_start: 0.7958 (mmp) cc_final: 0.6852 (mtm)
REVERT: B  591 MET cc_start: 0.8571 (mtp) cc_final: 0.8340 (mtt)
REVERT: B  601 MET cc_start: 0.8981 (ttp) cc_final: 0.8779 (tmm)
REVERT: B  718 TRP cc_start: 0.7065 (t60) cc_final: 0.6363 (t60)
  outliers start: 10
  outliers final: 5
  residues processed: 159
  average time/residue: 0.0964
  time to fit residues: 22.8813
Evaluate side-chains
  154 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 147
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 GLN
Chi-restraints excluded: chain A residue  355 ASN
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  561 VAL
Chi-restraints excluded: chain A residue  601 MET
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain B residue  435 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 97 optimal weight:    0.6980
   chunk 95 optimal weight:    0.9990
   chunk 127 optimal weight:    5.9990
   chunk 122 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   chunk 111 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0370
   chunk 6 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0370
   chunk 145 optimal weight:    6.9990
   overall best weight:    0.5536

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

Flipped N/Q/H residues before XYZ refinement:
B  68 GLN
B 305 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.135215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.100677 restraints weight = 27053.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 2.46
r_work: 0.2863 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2857
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2857 r_free = 0.2857    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2857 r_free = 0.2857    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2857
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.3247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.141  12518  Z= 0.111
  Angle     :  0.595  10.984  17109  Z= 0.287
  Chirality :  0.039   0.203   1807
  Planarity :  0.004   0.041   2113
  Dihedral  :  8.815  79.794   1874
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 13.40 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.23), residues: 1488
  helix:  0.26 (0.17), residues: 984
  sheet:  None (None), residues: 0
  loop : -1.80 (0.29), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 432 
 TYR   0.016   0.001   TYR A 285 
 PHE   0.012   0.001   PHE A  24 
 TRP   0.020   0.001   TRP B 215 
 HIS   0.004   0.001   HIS A 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (12514)
  covalent geometry    : angle       0.59479 (17109)
  hydrogen bonds       : bond        0.03203 (  611)
  hydrogen bonds       : angle       4.00880 ( 1764)
  Misc. bond           : bond        0.12600 (    4)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 155
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.3439 (ptp) cc_final: 0.2598 (ttp)
REVERT: A   67 MET cc_start: 0.8772 (mtt) cc_final: 0.8521 (mtt)
REVERT: A  280 ARG cc_start: 0.7677 (mtm110) cc_final: 0.7077 (mtm110)
REVERT: A  320 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7815 (mp10)
REVERT: A  445 LYS cc_start: 0.6241 (ptmt) cc_final: 0.4962 (mmtm)
REVERT: A  601 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8255 (tmm)
REVERT: A  718 TRP cc_start: 0.7429 (t60) cc_final: 0.6540 (t60)
REVERT: B    1 MET cc_start: 0.3140 (ptp) cc_final: 0.2614 (ptp)
REVERT: B  515 MET cc_start: 0.7923 (mmp) cc_final: 0.6818 (mtm)
REVERT: B  591 MET cc_start: 0.8531 (mtp) cc_final: 0.8291 (mtt)
REVERT: B  718 TRP cc_start: 0.7014 (t60) cc_final: 0.6322 (t60)
  outliers start: 11
  outliers final: 8
  residues processed: 159
  average time/residue: 0.1088
  time to fit residues: 25.3410
Evaluate side-chains
  160 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 150
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  302 PHE
Chi-restraints excluded: chain A residue  320 GLN
Chi-restraints excluded: chain A residue  355 ASN
Chi-restraints excluded: chain A residue  561 VAL
Chi-restraints excluded: chain A residue  601 MET
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  435 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 45 optimal weight:    0.2980
   chunk 5 optimal weight:    5.9990
   chunk 140 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 87 optimal weight:    7.9990
   chunk 4 optimal weight:    6.9990
   chunk 10 optimal weight:    0.4980
   chunk 38 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 129 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B 305 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.134746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.101062 restraints weight = 25711.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 2.35
r_work: 0.2890 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2881
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2881
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.3441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.139  12518  Z= 0.117
  Angle     :  0.597  10.621  17109  Z= 0.286
  Chirality :  0.039   0.191   1807
  Planarity :  0.004   0.041   2113
  Dihedral  :  8.670  79.479   1874
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 13.66 %
    Favored  : 85.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.23), residues: 1488
  helix:  0.34 (0.17), residues: 1000
  sheet:  None (None), residues: 0
  loop : -1.64 (0.30), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 358 
 TYR   0.014   0.001   TYR A 127 
 PHE   0.011   0.001   PHE A 461 
 TRP   0.019   0.001   TRP B 215 
 HIS   0.004   0.001   HIS A 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (12514)
  covalent geometry    : angle       0.59741 (17109)
  hydrogen bonds       : bond        0.03210 (  611)
  hydrogen bonds       : angle       4.01293 ( 1764)
  Misc. bond           : bond        0.12032 (    4)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 153
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3488 (ptp) cc_final: 0.2639 (ttp)
REVERT: A   67 MET cc_start: 0.8796 (mtt) cc_final: 0.8533 (mtt)
REVERT: A  280 ARG cc_start: 0.7706 (mtm110) cc_final: 0.7221 (mtm110)
REVERT: A  320 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7839 (mp10)
REVERT: A  445 LYS cc_start: 0.6305 (ptmt) cc_final: 0.5054 (mmtm)
REVERT: A  601 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8247 (tmm)
REVERT: A  718 TRP cc_start: 0.7413 (t60) cc_final: 0.6591 (t60)
REVERT: B    1 MET cc_start: 0.3168 (ptp) cc_final: 0.2622 (ptp)
REVERT: B   32 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7947 (tt0)
REVERT: B  355 ASN cc_start: 0.8988 (t0) cc_final: 0.8645 (t0)
REVERT: B  515 MET cc_start: 0.7872 (mmp) cc_final: 0.6791 (mtm)
REVERT: B  591 MET cc_start: 0.8508 (mtp) cc_final: 0.8279 (mtt)
REVERT: B  718 TRP cc_start: 0.7032 (t60) cc_final: 0.6353 (t60)
  outliers start: 14
  outliers final: 9
  residues processed: 161
  average time/residue: 0.1094
  time to fit residues: 25.9744
Evaluate side-chains
  159 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 148
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  302 PHE
Chi-restraints excluded: chain A residue  320 GLN
Chi-restraints excluded: chain A residue  483 TRP
Chi-restraints excluded: chain A residue  561 VAL
Chi-restraints excluded: chain A residue  601 MET
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  435 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 58 optimal weight:    0.2980
   chunk 70 optimal weight:    0.9990
   chunk 131 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 132 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 113 optimal weight:    5.9990
   chunk 107 optimal weight:    4.9990
   chunk 78 optimal weight:    5.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 224 HIS    A
B 305 HIS
** B 473 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 = 0.3483 r_free = 0.3483 target = 0.133736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.099728 restraints weight = 31139.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 2.78
r_work: 0.2829 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2822
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2822
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.3654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.143  12518  Z= 0.117
  Angle     :  0.593  10.464  17109  Z= 0.285
  Chirality :  0.039   0.197   1807
  Planarity :  0.004   0.042   2113
  Dihedral  :  8.500  79.750   1874
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.66 %
    Favored  : 85.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.23), residues: 1488
  helix:  0.48 (0.17), residues: 992
  sheet:  None (None), residues: 0
  loop : -1.60 (0.30), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 358 
 TYR   0.014   0.001   TYR B 468 
 PHE   0.010   0.001   PHE A 461 
 TRP   0.019   0.001   TRP B 215 
 HIS   0.004   0.001   HIS A 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (12514)
  covalent geometry    : angle       0.59253 (17109)
  hydrogen bonds       : bond        0.03205 (  611)
  hydrogen bonds       : angle       3.96889 ( 1764)
  Misc. bond           : bond        0.12294 (    4)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 150
  time to evaluate  : 0.420 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3290 (ptp) cc_final: 0.2787 (ptp)
REVERT: A  280 ARG cc_start: 0.7631 (mtm110) cc_final: 0.7083 (mtm110)
REVERT: A  320 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7895 (mp10)
REVERT: A  428 VAL cc_start: 0.8093 (t) cc_final: 0.7884 (p)
REVERT: A  445 LYS cc_start: 0.6220 (ptmt) cc_final: 0.4882 (mmtm)
REVERT: A  601 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8332 (tmm)
REVERT: A  718 TRP cc_start: 0.7532 (t60) cc_final: 0.6648 (t60)
REVERT: B    1 MET cc_start: 0.3096 (ptp) cc_final: 0.2565 (ptp)
REVERT: B   32 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8034 (tt0)
REVERT: B  305 HIS cc_start: 0.7834 (t-90) cc_final: 0.6802 (t70)
REVERT: B  355 ASN cc_start: 0.8984 (t0) cc_final: 0.8639 (t0)
REVERT: B  515 MET cc_start: 0.7989 (mmp) cc_final: 0.6849 (mtm)
REVERT: B  591 MET cc_start: 0.8533 (mtp) cc_final: 0.8316 (mtt)
REVERT: B  718 TRP cc_start: 0.7160 (t60) cc_final: 0.6442 (t60)
  outliers start: 15
  outliers final: 11
  residues processed: 158
  average time/residue: 0.1053
  time to fit residues: 24.8021
Evaluate side-chains
  156 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LYS
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  302 PHE
Chi-restraints excluded: chain A residue  320 GLN
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  483 TRP
Chi-restraints excluded: chain A residue  561 VAL
Chi-restraints excluded: chain A residue  601 MET
Chi-restraints excluded: chain A residue  620 ILE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  435 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   chunk 124 optimal weight:    1.9990
   chunk 128 optimal weight:    0.5980
   chunk 77 optimal weight:    0.0040
   chunk 11 optimal weight:    9.9990
   chunk 71 optimal weight:    8.9990
   chunk 99 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9990
   chunk 127 optimal weight:    0.9980
   overall best weight:    0.9196

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

Flipped N/Q/H residues before XYZ refinement:
B 214 ASN
** B 473 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 = 0.3509 r_free = 0.3509 target = 0.135687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.105086 restraints weight = 21832.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 2.07
r_work: 0.2887 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2877
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2877 r_free = 0.2877    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2877 r_free = 0.2877    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2877
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.3759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.147  12518  Z= 0.125
  Angle     :  0.596  10.290  17109  Z= 0.286
  Chirality :  0.039   0.165   1807
  Planarity :  0.004   0.042   2113
  Dihedral  :  8.475  80.070   1874
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 13.57 %
    Favored  : 85.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.23), residues: 1488
  helix:  0.53 (0.17), residues: 992
  sheet:  None (None), residues: 0
  loop : -1.56 (0.30), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 358 
 TYR   0.013   0.001   TYR B 468 
 PHE   0.012   0.001   PHE A 461 
 TRP   0.021   0.001   TRP B 215 
 HIS   0.004   0.001   HIS A 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (12514)
  covalent geometry    : angle       0.59550 (17109)
  hydrogen bonds       : bond        0.03264 (  611)
  hydrogen bonds       : angle       3.95860 ( 1764)
  Misc. bond           : bond        0.13358 (    4)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 0.474 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3392 (ptp) cc_final: 0.2898 (ptp)
REVERT: A  280 ARG cc_start: 0.7604 (mtm110) cc_final: 0.7073 (mtm110)
REVERT: A  286 LEU cc_start: 0.8654 (mp) cc_final: 0.8440 (mt)
REVERT: A  320 GLN cc_start: 0.8365 (pt0) cc_final: 0.7883 (mp10)
REVERT: A  428 VAL cc_start: 0.8189 (t) cc_final: 0.7943 (p)
REVERT: A  445 LYS cc_start: 0.6267 (ptmt) cc_final: 0.5020 (mmtm)
REVERT: A  601 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8331 (tmm)
REVERT: A  718 TRP cc_start: 0.7443 (t60) cc_final: 0.6595 (t60)
REVERT: B    1 MET cc_start: 0.3255 (ptp) cc_final: 0.2715 (ptp)
REVERT: B   32 GLN cc_start: 0.8380 (mm-40) cc_final: 0.7973 (tt0)
REVERT: B  355 ASN cc_start: 0.8943 (t0) cc_final: 0.8616 (t0)
REVERT: B  515 MET cc_start: 0.7884 (mmp) cc_final: 0.6795 (mtm)
REVERT: B  591 MET cc_start: 0.8492 (mtp) cc_final: 0.8261 (mtt)
REVERT: B  718 TRP cc_start: 0.7101 (t60) cc_final: 0.6472 (t60)
  outliers start: 16
  outliers final: 14
  residues processed: 155
  average time/residue: 0.1093
  time to fit residues: 24.9911
Evaluate side-chains
  155 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 140
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LYS
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  483 TRP
Chi-restraints excluded: chain A residue  561 VAL
Chi-restraints excluded: chain A residue  601 MET
Chi-restraints excluded: chain A residue  620 ILE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  393 MET
Chi-restraints excluded: chain B residue  435 VAL
Chi-restraints excluded: chain B residue  494 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 103 optimal weight:    0.7980
   chunk 75 optimal weight:    6.9990
   chunk 94 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 105 optimal weight:    0.0980
   chunk 9 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
B  68 GLN
** B 473 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 = 0.3488 r_free = 0.3488 target = 0.134245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.100690 restraints weight = 26938.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 2.40
r_work: 0.2871 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2862
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2862 r_free = 0.2862    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2862 r_free = 0.2862    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2862
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.3892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.144  12518  Z= 0.116
  Angle     :  0.589  10.283  17109  Z= 0.282
  Chirality :  0.039   0.161   1807
  Planarity :  0.004   0.042   2113
  Dihedral  :  8.386  81.252   1874
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 14.09 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.23), residues: 1488
  helix:  0.62 (0.17), residues: 992
  sheet:  None (None), residues: 0
  loop : -1.55 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 358 
 TYR   0.013   0.001   TYR B 468 
 PHE   0.012   0.001   PHE B 635 
 TRP   0.018   0.001   TRP B 215 
 HIS   0.004   0.001   HIS A 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (12514)
  covalent geometry    : angle       0.58882 (17109)
  hydrogen bonds       : bond        0.03199 (  611)
  hydrogen bonds       : angle       3.93125 ( 1764)
  Misc. bond           : bond        0.12748 (    4)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 142
  time to evaluate  : 0.448 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3361 (ptp) cc_final: 0.2868 (ptp)
REVERT: A  280 ARG cc_start: 0.7610 (mtm110) cc_final: 0.7076 (mtm110)
REVERT: A  286 LEU cc_start: 0.8635 (mp) cc_final: 0.8423 (mt)
REVERT: A  320 GLN cc_start: 0.8396 (pt0) cc_final: 0.7915 (mp10)
REVERT: A  445 LYS cc_start: 0.6213 (ptmt) cc_final: 0.4951 (mmtm)
REVERT: A  601 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8431 (tmm)
REVERT: A  718 TRP cc_start: 0.7450 (t60) cc_final: 0.6596 (t60)
REVERT: B    1 MET cc_start: 0.3298 (ptp) cc_final: 0.2773 (ptp)
REVERT: B   15 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7759 (mm)
REVERT: B  355 ASN cc_start: 0.8954 (t0) cc_final: 0.8632 (t0)
REVERT: B  515 MET cc_start: 0.7937 (mmp) cc_final: 0.6829 (mtm)
REVERT: B  591 MET cc_start: 0.8503 (mtp) cc_final: 0.8292 (mtt)
REVERT: B  718 TRP cc_start: 0.7156 (t60) cc_final: 0.6502 (t60)
  outliers start: 12
  outliers final: 10
  residues processed: 151
  average time/residue: 0.1125
  time to fit residues: 24.8421
Evaluate side-chains
  150 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 138
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  483 TRP
Chi-restraints excluded: chain A residue  561 VAL
Chi-restraints excluded: chain A residue  601 MET
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  393 MET
Chi-restraints excluded: chain B residue  435 VAL
Chi-restraints excluded: chain B residue  494 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 5 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9990
   chunk 92 optimal weight:    0.0040
   chunk 147 optimal weight:    2.9990
   chunk 82 optimal weight:    0.1980
   chunk 117 optimal weight:    0.0570
   chunk 94 optimal weight:    0.1980
   chunk 145 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    0.2710

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

Flipped N/Q/H residues before XYZ refinement:
** B 473 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 = 0.3569 r_free = 0.3569 target = 0.140678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.107237 restraints weight = 34712.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 2.71
r_work: 0.2892 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2884
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2884
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.3999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.126  12518  Z= 0.099
  Angle     :  0.569  10.169  17109  Z= 0.273
  Chirality :  0.038   0.159   1807
  Planarity :  0.003   0.039   2113
  Dihedral  :  8.208  83.502   1874
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 14.00 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.23), residues: 1488
  helix:  0.81 (0.18), residues: 980
  sheet:  None (None), residues: 0
  loop : -1.58 (0.29), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 187 
 TYR   0.012   0.001   TYR B 638 
 PHE   0.011   0.001   PHE A 461 
 TRP   0.022   0.001   TRP B 215 
 HIS   0.004   0.001   HIS A 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (12514)
  covalent geometry    : angle       0.56925 (17109)
  hydrogen bonds       : bond        0.03019 (  611)
  hydrogen bonds       : angle       3.87474 ( 1764)
  Misc. bond           : bond        0.09975 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2766.61 seconds
wall clock time: 48 minutes 8.29 seconds (2888.29 seconds total)