Starting phenix.real_space_refine
on Wed Jul 30 14:53:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qq6_4619/07_2025/6qq6_4619.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qq6_4619/07_2025/6qq6_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_4619/07_2025/6qq6_4619.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qq6_4619/07_2025/6qq6_4619.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qq6_4619/07_2025/6qq6_4619.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qq6_4619/07_2025/6qq6_4619.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 13.84, per 1000 atoms: 1.14
  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: 3.36
  Conformation dependent library (CDL) restraints added in 3.2 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: 1.99
  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: 4.30

  Time building geometry restraints manager: 3.94 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 743 or resid 801 throug \ 
h 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 C24 or name C25 or name C26 or name C27 or name C28 or n \ 
ame C29 or name C3 or name C30 or name C4 or name C5 or name C6 or name C7 or na \ 
me 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 743 or resid 801 throug \ 
h 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 C24 or name C25 or name C26 or name C27 or name C28 or n \ 
ame C29 or name C3 or name C30 or name C4 or name C5 or name C6 or name C7 or na \ 
me 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:             1.270
  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:             0.030
  Extract box with map and model:          0.670
  Check model and map are aligned:         0.110
  Set scattering table:                    0.160
  Process input model:                     41.730
  Find NCS groups from input model:        0.630
  Set up NCS constraints:                  0.090
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.290
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.024   0.002   TRP A 215 
 HIS   0.007   0.002   HIS B 537 
 PHE   0.022   0.002   PHE A 635 
 TYR   0.019   0.002   TYR A 468 
 ARG   0.002   0.000   ARG B 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15790 (  611)
  hydrogen bonds       : angle       6.99370 ( 1764)
  covalent geometry    : bond        0.00657 (12514)
  covalent geometry    : angle       1.07581 (17109)
  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  : 1.355 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.3616 (ptp) cc_final: 0.2964 (ttp)
REVERT: A  718 TRP cc_start: 0.6828 (t60) cc_final: 0.6101 (t60)
REVERT: B    1 MET cc_start: 0.3557 (ptp) cc_final: 0.3099 (ptp)
REVERT: B  355 ASN cc_start: 0.8773 (t0) cc_final: 0.8303 (t0)
REVERT: B  430 MET cc_start: 0.8193 (mmm) cc_final: 0.7888 (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: 0.2560
  time to fit residues: 79.7162
Evaluate side-chains
  158 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 1.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:    3.9990
   chunk 112 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 116 optimal weight:    0.9990
   chunk 44 optimal weight:   20.0000
   chunk 70 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 134 optimal weight:    0.8980
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 = 0.3447 r_free = 0.3447 target = 0.130491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.095200 restraints weight = 33660.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.2980 rms_B_bonded: 2.90
r_work: 0.2796 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2789
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.283  12518  Z= 0.179
  Angle     :  0.693   8.818  17109  Z= 0.343
  Chirality :  0.044   0.346   1807
  Planarity :  0.005   0.053   2113
  Dihedral  : 11.512  87.722   1874
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  9.36 %
    Favored  : 89.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.20), residues: 1488
  helix: -1.41 (0.15), residues: 1002
  sheet:  None (None), residues: 0
  loop : -2.68 (0.25), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 215 
 HIS   0.004   0.001   HIS B 537 
 PHE   0.016   0.001   PHE B 635 
 TYR   0.020   0.002   TYR B 108 
 ARG   0.009   0.001   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03765 (  611)
  hydrogen bonds       : angle       4.67011 ( 1764)
  covalent geometry    : bond        0.00416 (12514)
  covalent geometry    : angle       0.69287 (17109)
  Misc. bond           : bond        0.19746 (    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
  188 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 173
  time to evaluate  : 1.311 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.3239 (ptp) cc_final: 0.2529 (ttp)
REVERT: A  231 MET cc_start: 0.7680 (mmm) cc_final: 0.7190 (ttt)
REVERT: A  280 ARG cc_start: 0.7557 (mtm110) cc_final: 0.6997 (mtm110)
REVERT: A  320 GLN cc_start: 0.8040 (pt0) cc_final: 0.7385 (mp10)
REVERT: A  445 LYS cc_start: 0.6218 (ptmt) cc_final: 0.5975 (ptmt)
REVERT: A  579 ARG cc_start: 0.8616 (ttm-80) cc_final: 0.8415 (ttm-80)
REVERT: A  708 MET cc_start: 0.8627 (mmt) cc_final: 0.8398 (tpt)
REVERT: A  718 TRP cc_start: 0.7460 (t60) cc_final: 0.6530 (t60)
REVERT: B    1 MET cc_start: 0.3047 (ptp) cc_final: 0.2512 (ptp)
REVERT: B  231 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7269 (ttp)
REVERT: B  355 ASN cc_start: 0.9161 (t0) cc_final: 0.8633 (t0)
REVERT: B  430 MET cc_start: 0.8652 (mmm) cc_final: 0.8263 (tpt)
REVERT: B  718 TRP cc_start: 0.6982 (t60) cc_final: 0.6236 (t60)
  outliers start: 15
  outliers final: 6
  residues processed: 181
  average time/residue: 0.2558
  time to fit residues: 67.2001
Evaluate side-chains
  163 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 156
  time to evaluate  : 1.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 SER
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  298 LEU
Chi-restraints excluded: chain B residue  435 VAL
Chi-restraints excluded: chain B residue  646 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 84 optimal weight:    0.5980
   chunk 136 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 146 optimal weight:    0.8980
   chunk 88 optimal weight:    2.9990
   chunk 115 optimal weight:    0.7980
   chunk 114 optimal weight:    0.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.130237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.095979 restraints weight = 35862.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.2995 rms_B_bonded: 2.91
r_work: 0.2772 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2762
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2762 r_free = 0.2762    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2762 r_free = 0.2762    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2762
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.245  12518  Z= 0.153
  Angle     :  0.665  12.147  17109  Z= 0.318
  Chirality :  0.041   0.247   1807
  Planarity :  0.004   0.045   2113
  Dihedral  : 10.198  82.501   1874
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 11.34 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.21), residues: 1488
  helix: -0.73 (0.16), residues: 1002
  sheet:  None (None), residues: 0
  loop : -2.28 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 215 
 HIS   0.003   0.001   HIS A 331 
 PHE   0.014   0.001   PHE B 635 
 TYR   0.019   0.002   TYR B 108 
 ARG   0.006   0.000   ARG A 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03720 (  611)
  hydrogen bonds       : angle       4.45321 ( 1764)
  covalent geometry    : bond        0.00362 (12514)
  covalent geometry    : angle       0.66502 (17109)
  Misc. bond           : bond        0.20220 (    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
  162 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 151
  time to evaluate  : 1.223 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3275 (ptp) cc_final: 0.2634 (ttp)
REVERT: A   39 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6588 (mm-30)
REVERT: A   67 MET cc_start: 0.8800 (mtt) cc_final: 0.8565 (mtt)
REVERT: A  231 MET cc_start: 0.7627 (mmm) cc_final: 0.7134 (ttt)
REVERT: A  280 ARG cc_start: 0.7681 (mtm110) cc_final: 0.7043 (mtm110)
REVERT: A  320 GLN cc_start: 0.8195 (pt0) cc_final: 0.7569 (mp10)
REVERT: A  494 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8159 (tm-30)
REVERT: A  718 TRP cc_start: 0.7499 (t60) cc_final: 0.6582 (t60)
REVERT: B    1 MET cc_start: 0.3110 (ptp) cc_final: 0.2547 (ptp)
REVERT: B  231 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7299 (ttp)
REVERT: B  355 ASN cc_start: 0.9161 (t0) cc_final: 0.8685 (t0)
REVERT: B  591 MET cc_start: 0.8598 (mtp) cc_final: 0.8339 (mtt)
REVERT: B  718 TRP cc_start: 0.7128 (t60) cc_final: 0.6404 (t60)
  outliers start: 11
  outliers final: 9
  residues processed: 156
  average time/residue: 0.2401
  time to fit residues: 54.8581
Evaluate side-chains
  150 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
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  561 VAL
Chi-restraints excluded: chain A residue  584 GLU
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  435 VAL
Chi-restraints excluded: chain B residue  646 THR
Chi-restraints excluded: chain B residue  708 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 104 optimal weight:    0.8980
   chunk 35 optimal weight:    6.9990
   chunk 11 optimal weight:    8.9990
   chunk 21 optimal weight:    0.4980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  68 GLN
B 214 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.132213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.097788 restraints weight = 25738.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3014 rms_B_bonded: 2.46
r_work: 0.2832 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2822
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2822
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.3043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.181  12518  Z= 0.124
  Angle     :  0.605   7.331  17109  Z= 0.295
  Chirality :  0.040   0.267   1807
  Planarity :  0.004   0.046   2113
  Dihedral  :  9.528  81.046   1874
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 12.11 %
    Favored  : 86.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.22), residues: 1488
  helix: -0.34 (0.17), residues: 1000
  sheet:  None (None), residues: 0
  loop : -2.06 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 215 
 HIS   0.004   0.001   HIS A 537 
 PHE   0.012   0.001   PHE B 194 
 TYR   0.029   0.001   TYR B 406 
 ARG   0.005   0.000   ARG B 432 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03333 (  611)
  hydrogen bonds       : angle       4.20756 ( 1764)
  covalent geometry    : bond        0.00299 (12514)
  covalent geometry    : angle       0.60515 (17109)
  Misc. bond           : bond        0.15783 (    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
  165 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 152
  time to evaluate  : 1.215 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3286 (ptp) cc_final: 0.2537 (ttp)
REVERT: A   67 MET cc_start: 0.8807 (mtt) cc_final: 0.8558 (mtt)
REVERT: A  231 MET cc_start: 0.7504 (mmm) cc_final: 0.7106 (ttt)
REVERT: A  280 ARG cc_start: 0.7687 (mtm110) cc_final: 0.7101 (mtm110)
REVERT: A  320 GLN cc_start: 0.8190 (pt0) cc_final: 0.7582 (mp10)
REVERT: A  445 LYS cc_start: 0.6193 (ptmt) cc_final: 0.4890 (mmtm)
REVERT: A  610 MET cc_start: 0.8345 (ttp) cc_final: 0.8115 (ttp)
REVERT: A  718 TRP cc_start: 0.7438 (t60) cc_final: 0.6576 (t60)
REVERT: B    1 MET cc_start: 0.3131 (ptp) cc_final: 0.2577 (ptp)
REVERT: B  355 ASN cc_start: 0.9132 (t0) cc_final: 0.8707 (t0)
REVERT: B  515 MET cc_start: 0.7945 (mmp) cc_final: 0.6882 (mtm)
REVERT: B  591 MET cc_start: 0.8503 (mtp) cc_final: 0.8249 (mtt)
REVERT: B  680 PHE cc_start: 0.8921 (m-80) cc_final: 0.8709 (m-80)
REVERT: B  718 TRP cc_start: 0.7026 (t60) cc_final: 0.6326 (t60)
  outliers start: 13
  outliers final: 8
  residues processed: 159
  average time/residue: 0.2315
  time to fit residues: 54.3281
Evaluate side-chains
  150 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 142
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 115 optimal weight:    0.9990
   chunk 113 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 143 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 16 optimal weight:    8.9990
   chunk 103 optimal weight:    0.6980
   chunk 79 optimal weight:    7.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.132188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.096508 restraints weight = 34264.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 2.97
r_work: 0.2813 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2804
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2804 r_free = 0.2804    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2804 r_free = 0.2804    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2804
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.3329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.177  12518  Z= 0.126
  Angle     :  0.611   8.795  17109  Z= 0.294
  Chirality :  0.040   0.220   1807
  Planarity :  0.004   0.044   2113
  Dihedral  :  9.225  80.432   1874
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 13.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.22), residues: 1488
  helix: -0.04 (0.17), residues: 998
  sheet:  None (None), residues: 0
  loop : -1.92 (0.29), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 215 
 HIS   0.003   0.001   HIS A 537 
 PHE   0.012   0.001   PHE B 635 
 TYR   0.015   0.001   TYR B 406 
 ARG   0.004   0.000   ARG B 432 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03319 (  611)
  hydrogen bonds       : angle       4.11189 ( 1764)
  covalent geometry    : bond        0.00305 (12514)
  covalent geometry    : angle       0.61116 (17109)
  Misc. bond           : bond        0.15927 (    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
  161 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 152
  time to evaluate  : 1.206 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3223 (ptp) cc_final: 0.2371 (ttp)
REVERT: A   67 MET cc_start: 0.8854 (mtt) cc_final: 0.8589 (mtt)
REVERT: A  231 MET cc_start: 0.7491 (mmm) cc_final: 0.7077 (ttt)
REVERT: A  280 ARG cc_start: 0.7697 (mtm110) cc_final: 0.7092 (mtm110)
REVERT: A  320 GLN cc_start: 0.8275 (pt0) cc_final: 0.7716 (mp10)
REVERT: A  445 LYS cc_start: 0.6244 (ptmt) cc_final: 0.4994 (mmtm)
REVERT: A  601 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8411 (tmm)
REVERT: A  657 TYR cc_start: 0.8208 (t80) cc_final: 0.7965 (t80)
REVERT: A  718 TRP cc_start: 0.7498 (t60) cc_final: 0.6588 (t60)
REVERT: B    1 MET cc_start: 0.3074 (ptp) cc_final: 0.2515 (ptp)
REVERT: B   32 GLN cc_start: 0.8400 (mm-40) cc_final: 0.7988 (mt0)
REVERT: B  355 ASN cc_start: 0.9125 (t0) cc_final: 0.8713 (t0)
REVERT: B  477 MET cc_start: 0.8115 (ttp) cc_final: 0.7906 (tmm)
REVERT: B  515 MET cc_start: 0.8072 (mmp) cc_final: 0.6961 (mtm)
REVERT: B  591 MET cc_start: 0.8549 (mtp) cc_final: 0.8314 (mtt)
REVERT: B  680 PHE cc_start: 0.8973 (m-80) cc_final: 0.8679 (m-80)
REVERT: B  718 TRP cc_start: 0.7091 (t60) cc_final: 0.6377 (t60)
  outliers start: 9
  outliers final: 7
  residues processed: 157
  average time/residue: 0.2250
  time to fit residues: 52.1318
Evaluate side-chains
  148 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 140
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 106 optimal weight:    0.7980
   chunk 73 optimal weight:    0.8980
   chunk 87 optimal weight:    7.9990
   chunk 111 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   chunk 77 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 75 optimal weight:    6.9990
   chunk 113 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  68 GLN
B 214 ASN
B 305 HIS
** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.132855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.096395 restraints weight = 37610.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 3.22
r_work: 0.2793 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2781
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2781 r_free = 0.2781    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2781 r_free = 0.2781    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2781
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.3522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.148  12518  Z= 0.117
  Angle     :  0.591   7.658  17109  Z= 0.286
  Chirality :  0.040   0.165   1807
  Planarity :  0.004   0.044   2113
  Dihedral  :  8.873  79.813   1874
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 13.92 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.23), residues: 1488
  helix:  0.17 (0.17), residues: 1000
  sheet:  None (None), residues: 0
  loop : -1.76 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 215 
 HIS   0.004   0.001   HIS A 537 
 PHE   0.011   0.001   PHE A 461 
 TYR   0.025   0.001   TYR B 406 
 ARG   0.007   0.000   ARG A 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03198 (  611)
  hydrogen bonds       : angle       4.01060 ( 1764)
  covalent geometry    : bond        0.00284 (12514)
  covalent geometry    : angle       0.59116 (17109)
  Misc. bond           : bond        0.14378 (    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
  154 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 145
  time to evaluate  : 1.295 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3362 (ptp) cc_final: 0.2845 (ptp)
REVERT: A   67 MET cc_start: 0.8794 (mtt) cc_final: 0.8509 (mtt)
REVERT: A  231 MET cc_start: 0.7520 (mmm) cc_final: 0.7127 (ttt)
REVERT: A  280 ARG cc_start: 0.7734 (mtm110) cc_final: 0.7239 (mtm110)
REVERT: A  320 GLN cc_start: 0.8313 (pt0) cc_final: 0.7766 (mp10)
REVERT: A  445 LYS cc_start: 0.6137 (ptmt) cc_final: 0.4887 (mmtm)
REVERT: A  601 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8418 (tmm)
REVERT: A  718 TRP cc_start: 0.7591 (t60) cc_final: 0.6688 (t60)
REVERT: B    1 MET cc_start: 0.3124 (ptp) cc_final: 0.2570 (ptp)
REVERT: B   32 GLN cc_start: 0.8394 (mm-40) cc_final: 0.8008 (mt0)
REVERT: B  355 ASN cc_start: 0.9077 (t0) cc_final: 0.8673 (t0)
REVERT: B  515 MET cc_start: 0.8081 (mmp) cc_final: 0.6968 (mtm)
REVERT: B  591 MET cc_start: 0.8609 (mtp) cc_final: 0.8406 (mtt)
REVERT: B  680 PHE cc_start: 0.8976 (m-80) cc_final: 0.8680 (m-80)
REVERT: B  718 TRP cc_start: 0.7235 (t60) cc_final: 0.6491 (t60)
  outliers start: 9
  outliers final: 8
  residues processed: 152
  average time/residue: 0.2508
  time to fit residues: 55.7198
Evaluate side-chains
  145 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 136
  time to evaluate  : 1.301 
-------------------------------------------------------------------------------
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  561 VAL
Chi-restraints excluded: chain A residue  601 MET
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  401 LEU
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 115 optimal weight:    3.9990
   chunk 123 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 142 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 98 optimal weight:    3.9990
   chunk 137 optimal weight:    0.5980
   chunk 88 optimal weight:    5.9990
   chunk 135 optimal weight:    0.0670
   chunk 100 optimal weight:    6.9990
   overall best weight:    1.2522

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
B 224 HIS    A
B 305 HIS
** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.131257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.094640 restraints weight = 34108.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 3.04
r_work: 0.2787 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2778
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2778
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.3669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.197  12518  Z= 0.145
  Angle     :  0.622  11.111  17109  Z= 0.298
  Chirality :  0.041   0.166   1807
  Planarity :  0.004   0.045   2113
  Dihedral  :  8.866  80.039   1874
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 14.00 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.23), residues: 1488
  helix:  0.26 (0.17), residues: 1000
  sheet:  None (None), residues: 0
  loop : -1.66 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 215 
 HIS   0.004   0.001   HIS A 537 
 PHE   0.013   0.001   PHE B 194 
 TYR   0.015   0.001   TYR B 406 
 ARG   0.007   0.000   ARG A 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03377 (  611)
  hydrogen bonds       : angle       4.05249 ( 1764)
  covalent geometry    : bond        0.00355 (12514)
  covalent geometry    : angle       0.62160 (17109)
  Misc. bond           : bond        0.17404 (    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
  156 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 144
  time to evaluate  : 1.202 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3187 (ptp) cc_final: 0.2668 (ptp)
REVERT: A  231 MET cc_start: 0.7555 (mmm) cc_final: 0.7057 (ttt)
REVERT: A  280 ARG cc_start: 0.7764 (mtm110) cc_final: 0.7193 (mtm110)
REVERT: A  320 GLN cc_start: 0.8365 (pt0) cc_final: 0.7805 (mp10)
REVERT: A  445 LYS cc_start: 0.6271 (ptmt) cc_final: 0.4958 (mmtm)
REVERT: A  601 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8485 (tmm)
REVERT: A  718 TRP cc_start: 0.7520 (t60) cc_final: 0.6592 (t60)
REVERT: B    1 MET cc_start: 0.3094 (ptp) cc_final: 0.2543 (ptp)
REVERT: B   32 GLN cc_start: 0.8396 (mm-40) cc_final: 0.7987 (mt0)
REVERT: B  355 ASN cc_start: 0.9085 (t0) cc_final: 0.8682 (t0)
REVERT: B  515 MET cc_start: 0.8078 (mmp) cc_final: 0.6961 (mtm)
REVERT: B  591 MET cc_start: 0.8571 (mtp) cc_final: 0.8360 (mtt)
REVERT: B  718 TRP cc_start: 0.7240 (t60) cc_final: 0.6553 (t60)
  outliers start: 12
  outliers final: 10
  residues processed: 154
  average time/residue: 0.2349
  time to fit residues: 53.1232
Evaluate side-chains
  149 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 138
  time to evaluate  : 1.355 
-------------------------------------------------------------------------------
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  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 A residue  716 LEU
Chi-restraints excluded: chain B residue   84 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 24 optimal weight:    0.6980
   chunk 129 optimal weight:    0.9980
   chunk 52 optimal weight:    0.7980
   chunk 36 optimal weight:    8.9990
   chunk 80 optimal weight:    2.9990
   chunk 78 optimal weight:   10.0000
   chunk 50 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 117 optimal weight:    0.0670
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
B 214 ASN
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 = 0.3541 r_free = 0.3541 target = 0.138337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.105492 restraints weight = 34839.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 2.76
r_work: 0.2848 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2839
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2839
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.3811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.149  12518  Z= 0.111
  Angle     :  0.588   9.703  17109  Z= 0.283
  Chirality :  0.039   0.180   1807
  Planarity :  0.004   0.043   2113
  Dihedral  :  8.625  81.367   1874
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.23), residues: 1488
  helix:  0.50 (0.17), residues: 988
  sheet:  None (None), residues: 0
  loop : -1.60 (0.29), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 215 
 HIS   0.004   0.001   HIS A 537 
 PHE   0.012   0.001   PHE A 461 
 TYR   0.012   0.001   TYR A 468 
 ARG   0.006   0.000   ARG A 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03132 (  611)
  hydrogen bonds       : angle       3.97264 ( 1764)
  covalent geometry    : bond        0.00267 (12514)
  covalent geometry    : angle       0.58823 (17109)
  Misc. bond           : bond        0.13543 (    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
  157 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 1.322 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3185 (ptp) cc_final: 0.2672 (ptp)
REVERT: A  231 MET cc_start: 0.7426 (mmm) cc_final: 0.7100 (ttt)
REVERT: A  280 ARG cc_start: 0.7632 (mtm110) cc_final: 0.7097 (mtm110)
REVERT: A  320 GLN cc_start: 0.8339 (pt0) cc_final: 0.7756 (mp10)
REVERT: A  445 LYS cc_start: 0.6315 (ptmt) cc_final: 0.5022 (mmtm)
REVERT: A  601 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8359 (tmm)
REVERT: A  718 TRP cc_start: 0.7482 (t60) cc_final: 0.6615 (t60)
REVERT: B    1 MET cc_start: 0.3215 (ptp) cc_final: 0.2677 (ptp)
REVERT: B   32 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8037 (tt0)
REVERT: B  355 ASN cc_start: 0.9037 (t0) cc_final: 0.8671 (t0)
REVERT: B  515 MET cc_start: 0.8049 (mmp) cc_final: 0.6943 (mtm)
REVERT: B  718 TRP cc_start: 0.7161 (t60) cc_final: 0.6506 (t60)
  outliers start: 15
  outliers final: 11
  residues processed: 153
  average time/residue: 0.2452
  time to fit residues: 54.9995
Evaluate side-chains
  148 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 1.205 
-------------------------------------------------------------------------------
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  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   84 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 21 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.3418 r_free = 0.3418 target = 0.127739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.094500 restraints weight = 28118.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 2.50
r_work: 0.2737 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.3919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.327  12518  Z= 0.252
  Angle     :  0.717  14.054  17109  Z= 0.343
  Chirality :  0.046   0.190   1807
  Planarity :  0.004   0.055   2113
  Dihedral  :  9.065  76.974   1874
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 14.18 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.22), residues: 1488
  helix:  0.06 (0.17), residues: 1012
  sheet:  None (None), residues: 0
  loop : -1.55 (0.30), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 215 
 HIS   0.004   0.001   HIS A 537 
 PHE   0.017   0.001   PHE B 635 
 TYR   0.021   0.002   TYR B 618 
 ARG   0.007   0.001   ARG A 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03967 (  611)
  hydrogen bonds       : angle       4.21545 ( 1764)
  covalent geometry    : bond        0.00612 (12514)
  covalent geometry    : angle       0.71725 (17109)
  Misc. bond           : bond        0.25333 (    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
  151 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 136
  time to evaluate  : 1.269 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.3291 (ptp) cc_final: 0.2768 (ptp)
REVERT: A    5 ARG cc_start: 0.7048 (mtt-85) cc_final: 0.6677 (ttm-80)
REVERT: A  231 MET cc_start: 0.7705 (mmm) cc_final: 0.6979 (ttt)
REVERT: A  280 ARG cc_start: 0.7780 (mtm110) cc_final: 0.7185 (mtm110)
REVERT: A  320 GLN cc_start: 0.8529 (pt0) cc_final: 0.7937 (mp10)
REVERT: A  445 LYS cc_start: 0.6296 (ptmt) cc_final: 0.5016 (mmtm)
REVERT: A  601 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8639 (tmm)
REVERT: A  680 PHE cc_start: 0.8971 (m-80) cc_final: 0.8736 (m-80)
REVERT: A  718 TRP cc_start: 0.7529 (t60) cc_final: 0.6658 (t60)
REVERT: B    1 MET cc_start: 0.3439 (ptp) cc_final: 0.2888 (ptp)
REVERT: B  355 ASN cc_start: 0.9087 (t0) cc_final: 0.8681 (t0)
REVERT: B  445 LYS cc_start: 0.6641 (ptmt) cc_final: 0.5416 (mmtm)
REVERT: B  515 MET cc_start: 0.8076 (mmp) cc_final: 0.6990 (mtm)
REVERT: B  680 PHE cc_start: 0.8997 (m-80) cc_final: 0.8671 (m-80)
REVERT: B  718 TRP cc_start: 0.7202 (t60) cc_final: 0.6536 (t60)
  outliers start: 15
  outliers final: 10
  residues processed: 147
  average time/residue: 0.3125
  time to fit residues: 65.6556
Evaluate side-chains
  143 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 1.562 
-------------------------------------------------------------------------------
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  561 VAL
Chi-restraints excluded: chain A residue  601 MET
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  124 LYS
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 109 optimal weight:    0.9990
   chunk 129 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 121 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 105 optimal weight:   10.0000
   chunk 77 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3428 r_free = 0.3428 target = 0.129441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.095886 restraints weight = 36118.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 2.99
r_work: 0.2760 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2745
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2745 r_free = 0.2745    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2745 r_free = 0.2745    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2745
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.4013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.204  12518  Z= 0.128
  Angle     :  0.614   9.911  17109  Z= 0.297
  Chirality :  0.040   0.188   1807
  Planarity :  0.004   0.045   2113
  Dihedral  :  8.762  79.853   1874
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 14.43 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.23), residues: 1488
  helix:  0.36 (0.17), residues: 994
  sheet:  None (None), residues: 0
  loop : -1.51 (0.30), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 215 
 HIS   0.004   0.001   HIS A 537 
 PHE   0.013   0.001   PHE B 194 
 TYR   0.016   0.001   TYR B 108 
 ARG   0.007   0.000   ARG A 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03375 (  611)
  hydrogen bonds       : angle       4.08954 ( 1764)
  covalent geometry    : bond        0.00312 (12514)
  covalent geometry    : angle       0.61350 (17109)
  Misc. bond           : bond        0.18054 (    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
  150 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 138
  time to evaluate  : 2.107 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.3368 (ptp) cc_final: 0.2837 (ptp)
REVERT: A  231 MET cc_start: 0.7618 (mmm) cc_final: 0.7051 (ttt)
REVERT: A  280 ARG cc_start: 0.7718 (mtm110) cc_final: 0.7104 (mtm110)
REVERT: A  320 GLN cc_start: 0.8495 (pt0) cc_final: 0.7938 (mp10)
REVERT: A  445 LYS cc_start: 0.6479 (ptmt) cc_final: 0.5181 (mmtm)
REVERT: A  601 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8604 (tmm)
REVERT: A  718 TRP cc_start: 0.7494 (t60) cc_final: 0.6643 (t60)
REVERT: B    1 MET cc_start: 0.3459 (ptp) cc_final: 0.2917 (ptp)
REVERT: B  355 ASN cc_start: 0.9003 (t0) cc_final: 0.8644 (t0)
REVERT: B  445 LYS cc_start: 0.6666 (ptmt) cc_final: 0.5401 (mmtm)
REVERT: B  515 MET cc_start: 0.8187 (mmp) cc_final: 0.7081 (mtm)
REVERT: B  718 TRP cc_start: 0.7179 (t60) cc_final: 0.6523 (t60)
  outliers start: 12
  outliers final: 9
  residues processed: 148
  average time/residue: 0.3462
  time to fit residues: 74.7459
Evaluate side-chains
  142 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 132
  time to evaluate  : 1.229 
-------------------------------------------------------------------------------
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  561 VAL
Chi-restraints excluded: chain A residue  601 MET
Chi-restraints excluded: chain A residue  620 ILE
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  435 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 137 optimal weight:    0.7980
   chunk 85 optimal weight:    6.9990
   chunk 83 optimal weight:    0.6980
   chunk 93 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 90 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9990
   chunk 87 optimal weight:    2.9990
   chunk 114 optimal weight:    2.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
B  68 GLN
** 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 = 0.3433 r_free = 0.3433 target = 0.129997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.098487 restraints weight = 27980.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 2.25
r_work: 0.2819 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2811
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2811 r_free = 0.2811    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 = 0.2811 r_free = 0.2811    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2811
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.4087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.177  12518  Z= 0.127
  Angle     :  0.613  10.433  17109  Z= 0.294
  Chirality :  0.040   0.196   1807
  Planarity :  0.004   0.047   2113
  Dihedral  :  8.612  81.126   1874
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 14.35 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.23), residues: 1488
  helix:  0.47 (0.17), residues: 988
  sheet:  None (None), residues: 0
  loop : -1.50 (0.29), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 215 
 HIS   0.004   0.001   HIS A 537 
 PHE   0.013   0.001   PHE A 461 
 TYR   0.016   0.001   TYR B 108 
 ARG   0.007   0.000   ARG A 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03306 (  611)
  hydrogen bonds       : angle       4.05388 ( 1764)
  covalent geometry    : bond        0.00310 (12514)
  covalent geometry    : angle       0.61348 (17109)
  Misc. bond           : bond        0.16300 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6166.97 seconds
wall clock time: 109 minutes 32.40 seconds (6572.40 seconds total)