Starting phenix.real_space_refine
on Sun Jun 29 17:32:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u5y_41939/06_2025/8u5y_41939.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u5y_41939/06_2025/8u5y_41939.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u5y_41939/06_2025/8u5y_41939.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u5y_41939/06_2025/8u5y_41939.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u5y_41939/06_2025/8u5y_41939.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u5y_41939/06_2025/8u5y_41939.cif"
  }
  resolution = 3.01
  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=   0.003 sd=   0.012
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: 6
    Type Number    sf(0)   Gaussians
     P      16      5.49       5
     S      78      5.16       5
     C   11057      2.51       5
     N    2937      2.21       5
     O    3251      1.98       5
     H   17152      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 34491
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 11430
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 700, 11429
          Classifications: {'peptide': 700}
          Link IDs: {'PTRANS': 50, 'TRANS': 649}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 700, 11429
          Classifications: {'peptide': 700}
          Link IDs: {'PTRANS': 50, 'TRANS': 649}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 11575
    Chain: "A"
      Number of atoms: 11320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 697, 11320
          Classifications: {'peptide': 697}
          Link IDs: {'PTRANS': 50, 'TRANS': 646}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 11229
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 692, 11228
          Classifications: {'peptide': 692}
          Link IDs: {'PTRANS': 50, 'TRANS': 641}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 14
      Conformer: "B"
        Number of residues, atoms: 692, 11228
          Classifications: {'peptide': 692}
          Link IDs: {'PTRANS': 50, 'TRANS': 641}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 14
          bond proxies already assigned to first conformer: 11368
    Chain: "D"
      Number of atoms: 512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 512
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
  Time building chain proxies: 25.76, per 1000 atoms: 0.75
  Number of scatterers: 34491
  At special positions: 0
  Unit cell: (104.14, 142.68, 154.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      78     16.00
     P      16     15.00
     O    3251      8.00
     N    2937      7.00
     C   11057      6.00
     H   17152      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 9.14
  Conformation dependent library (CDL) restraints added in 4.0 seconds
  

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3998

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 13 sheets defined
      21.0% alpha, 17.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.56
  Creating SS restraints...
    Processing helix  chain 'B' and resid 44 through 53
    Processing helix  chain 'B' and resid 114 through 120
      removed outlier: 4.131A  pdb=" N   VAL B 118 " --> pdb=" O   LEU B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 174
    Processing helix  chain 'B' and resid 220 through 227
    Processing helix  chain 'B' and resid 282 through 287
    Processing helix  chain 'B' and resid 343 through 347
    Processing helix  chain 'B' and resid 348 through 352
    Processing helix  chain 'B' and resid 362 through 367
    Processing helix  chain 'B' and resid 425 through 430
    Processing helix  chain 'B' and resid 479 through 495
    Processing helix  chain 'B' and resid 515 through 521
    Processing helix  chain 'B' and resid 524 through 529
      removed outlier: 4.689A  pdb=" N   LEU B 529 " --> pdb=" O   VAL B 525 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 534 through 542
      removed outlier: 3.699A  pdb=" N   LEU B 542 " --> pdb=" O   GLU B 538 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 682 through 689
    Processing helix  chain 'B' and resid 702 through 706
      removed outlier: 3.815A  pdb=" N   ILE B 706 " --> pdb=" O   PRO B 703 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 711 through 713
      No H-bonds generated for 'chain 'B' and resid 711 through 713'
    Processing helix  chain 'B' and resid 714 through 721
    Processing helix  chain 'B' and resid 773 through 780
    Processing helix  chain 'B' and resid 807 through 822
      removed outlier: 3.820A  pdb=" N   LEU B 822 " --> pdb=" O   ALA B 818 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 56
    Processing helix  chain 'A' and resid 112 through 114
      No H-bonds generated for 'chain 'A' and resid 112 through 114'
    Processing helix  chain 'A' and resid 115 through 120
    Processing helix  chain 'A' and resid 220 through 227
    Processing helix  chain 'A' and resid 282 through 287
    Processing helix  chain 'A' and resid 343 through 347
    Processing helix  chain 'A' and resid 348 through 352
    Processing helix  chain 'A' and resid 362 through 369
      removed outlier: 3.867A  pdb=" N   ASP A 368 " --> pdb=" O   SER A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 430
    Processing helix  chain 'A' and resid 473 through 477
    Processing helix  chain 'A' and resid 479 through 495
      removed outlier: 3.930A  pdb=" N   LYS A 483 " --> pdb=" O   ASP A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 522
      removed outlier: 3.818A  pdb=" N   SER A 522 " --> pdb=" O   LYS A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 528
      removed outlier: 6.338A  pdb=" N   GLU A 526 " --> pdb=" O   ILE A 523 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU A 528 " --> pdb=" O   VAL A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 542
      removed outlier: 3.589A  pdb=" N   LEU A 542 " --> pdb=" O   GLU A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 689
    Processing helix  chain 'A' and resid 702 through 706
      removed outlier: 3.775A  pdb=" N   ILE A 706 " --> pdb=" O   PRO A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 723
    Processing helix  chain 'A' and resid 738 through 742
      removed outlier: 3.816A  pdb=" N   PHE A 742 " --> pdb=" O   LEU A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 773 through 780
    Processing helix  chain 'A' and resid 809 through 822
      removed outlier: 3.623A  pdb=" N   LEU A 822 " --> pdb=" O   ALA A 818 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 54
    Processing helix  chain 'C' and resid 112 through 114
      No H-bonds generated for 'chain 'C' and resid 112 through 114'
    Processing helix  chain 'C' and resid 115 through 120
    Processing helix  chain 'C' and resid 170 through 175
    Processing helix  chain 'C' and resid 220 through 227
    Processing helix  chain 'C' and resid 282 through 287
    Processing helix  chain 'C' and resid 362 through 367
    Processing helix  chain 'C' and resid 425 through 430
    Processing helix  chain 'C' and resid 473 through 477
      removed outlier: 3.545A  pdb=" N   THR C 477 " --> pdb=" O   GLN C 474 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 479 through 495
    Processing helix  chain 'C' and resid 515 through 523
    Processing helix  chain 'C' and resid 534 through 542
    Processing helix  chain 'C' and resid 702 through 706
    Processing helix  chain 'C' and resid 711 through 714
    Processing helix  chain 'C' and resid 715 through 722
      removed outlier: 3.736A  pdb=" N   TYR C 722 " --> pdb=" O   LEU C 718 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 738 through 742
    Processing helix  chain 'C' and resid 773 through 780
    Processing helix  chain 'C' and resid 807 through 822
      removed outlier: 4.498A  pdb=" N   GLY C 813 " --> pdb=" O   ARG C 809 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   ILE C 816 " --> pdb=" O   ALA C 812 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU C 822 " --> pdb=" O   ALA C 818 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 128 through 129
      removed outlier: 5.595A  pdb=" N   VAL B  71 " --> pdb=" O   SER B 100 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   SER B 100 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ALA B  73 " --> pdb=" O   THR B  98 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   TYR B  95 " --> pdb=" O   LEU B 110 " (cutoff:3.500A)
      removed outlier: 8.385A  pdb=" N   ILE B 150 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   TYR B 109 " --> pdb=" O   ILE B 150 " (cutoff:3.500A)
      removed outlier: 8.243A  pdb=" N   ASN B 152 " --> pdb=" O   TYR B 109 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   ARG B 133 " --> pdb=" O   ASP B 151 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   VAL B 153 " --> pdb=" O   ILE B 131 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   ILE B 131 " --> pdb=" O   VAL B 153 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 237 through 244
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 237 through 244
    current: chain 'B' and resid 261 through 269
      removed outlier: 3.520A  pdb=" N   GLY B 272 " --> pdb=" O   ASP B 269 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 272 through 278
    current: chain 'B' and resid 322 through 330
    Processing sheet with id=AA3, first strand: chain 'B' and resid 360 through 361
      removed outlier: 4.533A  pdb=" N   ILE B 378 " --> pdb=" O   THR B 361 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 375 through 384
    current: chain 'B' and resid 399 through 408
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 416 through 421
    current: chain 'B' and resid 455 through 460
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 455 through 460
    current: chain 'B' and resid 708 through 709
    Processing sheet with id=AA4, first strand: chain 'B' and resid 547 through 561
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 679 through 681
    current: chain 'B' and resid 762 through 768
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 762 through 768
    current: chain 'B' and resid 841 through 849
    Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129
      removed outlier: 6.309A  pdb=" N   THR A  98 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   VAL A  74 " --> pdb=" O   ASP A  96 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ASP A  96 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   ARG A  76 " --> pdb=" O   CYS A  94 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   CYS A  94 " --> pdb=" O   ARG A  76 " (cutoff:3.500A)
      removed outlier: 4.950A  pdb=" N   TYR A  95 " --> pdb=" O   LEU A 110 " (cutoff:3.500A)
      removed outlier: 10.792A  pdb=" N   LEU A 148 " --> pdb=" O   GLN A 105 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   LYS A 107 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 8.308A  pdb=" N   ILE A 150 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   TYR A 109 " --> pdb=" O   ILE A 150 " (cutoff:3.500A)
      removed outlier: 8.298A  pdb=" N   ASN A 152 " --> pdb=" O   TYR A 109 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   ARG A 133 " --> pdb=" O   ASP A 151 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   VAL A 153 " --> pdb=" O   ILE A 131 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ILE A 131 " --> pdb=" O   VAL A 153 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 237 through 244
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 237 through 244
    current: chain 'A' and resid 261 through 269
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 272 through 278
    current: chain 'A' and resid 322 through 327
    Processing sheet with id=AA7, first strand: chain 'A' and resid 360 through 361
      removed outlier: 4.592A  pdb=" N   ILE A 378 " --> pdb=" O   THR A 361 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   HIS A 406 " --> pdb=" O   VAL A 382 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   VAL A 384 " --> pdb=" O   TRP A 404 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   TRP A 404 " --> pdb=" O   VAL A 384 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ARG A 386 " --> pdb=" O   TYR A 402 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   TYR A 402 " --> pdb=" O   ARG A 386 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   GLN A 388 " --> pdb=" O   TRP A 400 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   TRP A 400 " --> pdb=" O   GLN A 388 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 416 through 421
    current: chain 'A' and resid 455 through 460
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 455 through 460
    current: chain 'A' and resid 708 through 709
    Processing sheet with id=AA8, first strand: chain 'A' and resid 547 through 562
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 679 through 681
    current: chain 'A' and resid 762 through 768
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 762 through 768
    current: chain 'A' and resid 841 through 849
    Processing sheet with id=AA9, first strand: chain 'C' and resid 93 through 100
      removed outlier: 4.156A  pdb=" N   ALA C  73 " --> pdb=" O   THR C  98 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   SER C 100 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 5.609A  pdb=" N   VAL C  71 " --> pdb=" O   SER C 100 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 109 through 110
      removed outlier: 6.378A  pdb=" N   TYR C 109 " --> pdb=" O   ILE C 150 " (cutoff:3.500A)
      removed outlier: 7.720A  pdb=" N   ASN C 152 " --> pdb=" O   TYR C 109 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   ARG C 133 " --> pdb=" O   ASP C 151 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 239 through 244
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 239 through 244
    current: chain 'C' and resid 261 through 268
    Processing sheet with id=AB3, first strand: chain 'C' and resid 375 through 384
      removed outlier: 6.178A  pdb=" N   HIS C 406 " --> pdb=" O   VAL C 382 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   VAL C 384 " --> pdb=" O   TRP C 404 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   TRP C 404 " --> pdb=" O   VAL C 384 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 418 through 421
    current: chain 'C' and resid 457 through 460
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 457 through 460
    current: chain 'C' and resid 708 through 709
    Processing sheet with id=AB4, first strand: chain 'C' and resid 679 through 681
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 679 through 681
    current: chain 'C' and resid 767 through 768
      removed outlier: 7.212A  pdb=" N   ALA C 767 " --> pdb=" O   LEU C 845 " (cutoff:3.500A)
      removed outlier: 8.451A  pdb=" N   LYS C 847 " --> pdb=" O   ALA C 767 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   LYS C 840 " --> pdb=" O   LEU C 836 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ILE C 830 " --> pdb=" O   HIS C 846 " (cutoff:3.500A)
      removed outlier: 5.294A  pdb=" N   ILE C 848 " --> pdb=" O   VAL C 828 " (cutoff:3.500A)
      removed outlier: 5.787A  pdb=" N   VAL C 828 " --> pdb=" O   ILE C 848 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ILE C 827 " --> pdb=" O   GLY C 554 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ILE C 550 " --> pdb=" O   LEU C 831 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   THR C 754 " --> pdb=" O   THR C 557 " (cutoff:3.500A)
      removed outlier: 5.772A  pdb=" N   ILE C 762 " --> pdb=" O   GLY C 757 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ASP C 694 " --> pdb=" O   ALA C 763 " (cutoff:3.500A)
      removed outlier: 8.424A  pdb=" N   ASP C 765 " --> pdb=" O   ASP C 694 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   LEU C 696 " --> pdb=" O   ASP C 765 " (cutoff:3.500A)

    318 hydrogen bonds defined for protein.
    849 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: 13.26

  Time building geometry restraints manager: 11.07 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 17089
        1.03 -     1.23: 91
        1.23 -     1.42: 7367
        1.42 -     1.61: 10295
        1.61 -     1.81: 114
  Bond restraints: 34956
  Sorted by residual:
  bond pdb=" N   HIS B 564 "
       pdb=" H   HIS B 564 "
    ideal  model  delta    sigma   weight residual
    0.860  1.035 -0.175 2.00e-02 2.50e+03 7.68e+01
  bond pdb=" N   SER B 566 "
       pdb=" H   SER B 566 "
    ideal  model  delta    sigma   weight residual
    0.860  1.035 -0.175 2.00e-02 2.50e+03 7.66e+01
  bond pdb=" N   SER B 565 "
       pdb=" H   SER B 565 "
    ideal  model  delta    sigma   weight residual
    0.860  1.035 -0.175 2.00e-02 2.50e+03 7.65e+01
  bond pdb=" NE2 HIS B 564 "
       pdb=" HE2 HIS B 564 "
    ideal  model  delta    sigma   weight residual
    0.860  1.015 -0.155 2.00e-02 2.50e+03 6.00e+01
  bond pdb=" CD2 HIS B 564 "
       pdb=" HD2 HIS B 564 "
    ideal  model  delta    sigma   weight residual
    0.930  1.082 -0.152 2.00e-02 2.50e+03 5.74e+01
  ... (remaining 34951 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 62302
        1.55 -     3.11: 944
        3.11 -     4.66: 121
        4.66 -     6.21: 3
        6.21 -     7.76: 1
  Bond angle restraints: 63371
  Sorted by residual:
  angle pdb=" N   PRO B 563 "
        pdb=" CA  PRO B 563 "
        pdb=" C   PRO B 563 "
      ideal   model   delta    sigma   weight residual
     112.47  104.71    7.76 2.06e+00 2.36e-01 1.42e+01
  angle pdb=" C   SER C 270 "
        pdb=" CA  SER C 270 "
        pdb=" CB  SER C 270 "
      ideal   model   delta    sigma   weight residual
     116.34  111.17    5.17 1.40e+00 5.10e-01 1.36e+01
  angle pdb=" N   VAL A 103 "
        pdb=" CA  VAL A 103 "
        pdb=" C   VAL A 103 "
      ideal   model   delta    sigma   weight residual
     111.67  108.25    3.42 9.50e-01 1.11e+00 1.30e+01
  angle pdb=" N   ILE A 428 "
        pdb=" CA  ILE A 428 "
        pdb=" C   ILE A 428 "
      ideal   model   delta    sigma   weight residual
     111.62  108.90    2.72 7.90e-01 1.60e+00 1.19e+01
  angle pdb=" N   VAL A  87 "
        pdb=" CA  VAL A  87 "
        pdb=" C   VAL A  87 "
      ideal   model   delta    sigma   weight residual
     112.35  108.36    3.99 1.20e+00 6.94e-01 1.10e+01
  ... (remaining 63366 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.23: 15907
       32.23 -    64.46: 521
       64.46 -    96.69: 19
       96.69 -   128.92: 0
      128.92 -   161.15: 1
  Dihedral angle restraints: 16448
    sinusoidal: 9147
      harmonic: 7301
  Sorted by residual:
  dihedral pdb=" C4'  DT D   5 "
           pdb=" C3'  DT D   5 "
           pdb=" O3'  DT D   5 "
           pdb=" P    DT D   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   58.85  161.15     1      3.50e+01 8.16e-04 1.53e+01
  dihedral pdb=" CA  ASP C 409 "
           pdb=" CB  ASP C 409 "
           pdb=" CG  ASP C 409 "
           pdb=" OD1 ASP C 409 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.55   58.55     1      2.00e+01 2.50e-03 1.15e+01
  dihedral pdb=" CB  GLU B 842 "
           pdb=" CG  GLU B 842 "
           pdb=" CD  GLU B 842 "
           pdb=" OE1 GLU B 842 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.11  -89.11     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 16445 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1538
       0.028 -    0.057: 719
       0.057 -    0.085: 152
       0.085 -    0.113: 196
       0.113 -    0.142: 61
  Chirality restraints: 2666
  Sorted by residual:
  chirality pdb=" CA  ILE A 342 "
            pdb=" N   ILE A 342 "
            pdb=" C   ILE A 342 "
            pdb=" CB  ILE A 342 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.02e-01
  chirality pdb=" CA  ILE B 706 "
            pdb=" N   ILE B 706 "
            pdb=" C   ILE B 706 "
            pdb=" CB  ILE B 706 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.92e-01
  chirality pdb=" CA  ILE A 340 "
            pdb=" N   ILE A 340 "
            pdb=" C   ILE A 340 "
            pdb=" CB  ILE A 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.64e-01
  ... (remaining 2663 not shown)

  Planarity restraints: 4988
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 207 "   -0.027 5.00e-02 4.00e+02   4.03e-02 2.59e+00
        pdb=" N   PRO A 208 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 208 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 208 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS C 283 "    0.026 5.00e-02 4.00e+02   3.97e-02 2.53e+00
        pdb=" N   PRO C 284 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO C 284 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO C 284 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 474 "    0.026 5.00e-02 4.00e+02   3.88e-02 2.41e+00
        pdb=" N   PRO B 475 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO B 475 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 475 "    0.022 5.00e-02 4.00e+02
  ... (remaining 4985 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.19: 1806
        2.19 -     2.79: 72593
        2.79 -     3.39: 98297
        3.39 -     4.00: 132454
        4.00 -     4.60: 199266
  Nonbonded interactions: 504416
  Sorted by model distance:
  nonbonded pdb=" O   VAL C 384 "
            pdb=" H   GLY C 504 "
     model   vdw
     1.585 2.450
  nonbonded pdb=" O   PRO B 513 "
            pdb=" HH  TYR B 849 "
     model   vdw
     1.626 2.450
  nonbonded pdb="HD22 ASN C 500 "
            pdb=" O   PRO C 796 "
     model   vdw
     1.627 2.450
  nonbonded pdb=" O   THR C 441 "
            pdb=" HG  SER C 464 "
     model   vdw
     1.644 2.450
  nonbonded pdb=" O   VAL B 384 "
            pdb=" H   GLY B 504 "
     model   vdw
     1.659 2.450
  ... (remaining 504411 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 43 through 154 or resid 156 through 564 or (resid 565 and  \ 
(name N or name CA or name C or name O or name CB or name H or name HA )) or res \ 
id 676 through 682 or (resid 683 and (name N or name CA or name C or name O or n \ 
ame CB or name CG or name CD or name OE1 or name NE2)) or (resid 691 and (name N \ 
 or name CA or name C or name O )) or (resid 692 and (name N or name CA or name  \ 
C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name HB2 \ 
 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or n \ 
ame HD22 or name HD23)) or resid 693 through 759 or (resid 760 through 761 and ( \ 
name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ 
d 762 through 825 or (resid 826 and (name N or name CA or name C or name O or na \ 
me CB or name H or name HA )) or resid 827 through 851))
  selection = (chain 'B' and (resid 43 through 138 or (resid 139 and (name N or name CA or nam \ 
e C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 143 and  \ 
(name N or name CA or name C or name O or name CB or name CG1 or name CG2 or nam \ 
e CD1)) or (resid 144 and (name N or name CA or name C or name O )) or resid 145 \ 
 through 154 or resid 156 through 451 or (resid 452 and (name N or name CA or na \ 
me C or name O or name CB or name H or name HA )) or resid 453 through 473 or (r \ 
esid 474 and (name N or name CA or name C or name O or name CB or name H or name \ 
 HA )) or resid 475 through 524 or (resid 525 and (name N or name CA or name C o \ 
r name O or name CB or name H or name HA )) or resid 526 through 564 or (resid 5 \ 
65 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ 
 or resid 676 through 682 or (resid 683 and (name N or name CA or name C or name \ 
 O or name CB or name CG or name CD or name OE1 or name NE2)) or (resid 691 and  \ 
(name N or name CA or name C or name O )) or (resid 692 and (name N or name CA o \ 
r name C or name O or name CB or name CG or name CD1 or name CD2 or name HA or n \ 
ame HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD \ 
21 or name HD22 or name HD23)) or resid 693 through 759 or (resid 760 through 76 \ 
1 and (name N or name CA or name C or name O or name CB or name H or name HA ))  \ 
or resid 762 through 825 or (resid 826 and (name N or name CA or name C or name  \ 
O or name CB or name H or name HA )) or resid 827 through 851))
  selection = (chain 'C' and (resid 43 through 138 or (resid 139 and (name N or name CA or nam \ 
e C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 143 and  \ 
(name N or name CA or name C or name O or name CB or name CG1 or name CG2 or nam \ 
e CD1)) or (resid 144 and (name N or name CA or name C or name O )) or resid 145 \ 
 through 154 or resid 156 through 451 or (resid 452 and (name N or name CA or na \ 
me C or name O or name CB or name H or name HA )) or resid 453 through 473 or (r \ 
esid 474 and (name N or name CA or name C or name O or name CB or name H or name \ 
 HA )) or resid 475 through 524 or (resid 525 and (name N or name CA or name C o \ 
r name O or name CB or name H or name HA )) or resid 526 through 851))
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.100
  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:             0.580
  Extract box with map and model:          1.360
  Check model and map are aligned:         0.250
  Set scattering table:                    0.290
  Process input model:                     83.400
  Find NCS groups from input model:        1.200
  Set up NCS constraints:                  0.130
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   98.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  17804  Z= 0.144
  Angle     :  0.569   7.765  24250  Z= 0.328
  Chirality :  0.043   0.142   2666
  Planarity :  0.004   0.040   3059
  Dihedral  : 14.423 161.147   6810
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 13.06 %
    Favored  : 86.37 %
  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: -1.43 (0.19), residues: 2073
  helix:  0.37 (0.31), residues: 306
  sheet: -1.64 (0.22), residues: 546
  loop : -0.91 (0.18), residues: 1221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 228 
 HIS   0.002   0.001   HIS B 564 
 PHE   0.007   0.001   PHE A 416 
 TYR   0.014   0.001   TYR B 509 
 ARG   0.002   0.000   ARG A 715 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20040 (  318)
  hydrogen bonds       : angle       8.45942 (  849)
  covalent geometry    : bond        0.00278 (17804)
  covalent geometry    : angle       0.56897 (24250)

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

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

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  452 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue SER  565 is missing expected H atoms. Skipping.
Evaluate side-chains
  162 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 151
  time to evaluate  : 3.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  224 LEU cc_start: 0.9076 (tp) cc_final: 0.8828 (tp)
REVERT: A   49 VAL cc_start: 0.9273 (t) cc_final: 0.8849 (p)
REVERT: A   89 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8470 (mmtt)
REVERT: A  103 VAL cc_start: 0.8434 (t) cc_final: 0.8174 (t)
REVERT: A  334 ASP cc_start: 0.8575 (m-30) cc_final: 0.8372 (m-30)
REVERT: C  695 HIS cc_start: 0.6082 (t70) cc_final: 0.5666 (t-170)
  outliers start: 11
  outliers final: 9
  residues processed: 162
  average time/residue: 1.0266
  time to fit residues: 227.3592
Evaluate side-chains
  116 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 2.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 CYS
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  283 CYS
Chi-restraints excluded: chain A residue  373 CYS
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  515 THR
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain C residue  341 ILE
Chi-restraints excluded: chain C residue  347 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 209
   random chunks:
   chunk 176 optimal weight:    0.6980
   chunk 158 optimal weight:    4.9990
   chunk 87 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 106 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 163 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 99 optimal weight:    0.6980
   chunk 121 optimal weight:    1.9990
   chunk 189 optimal weight:    4.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.083015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.063436 restraints weight = 150460.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 3.13
r_work: 0.3143 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3146
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3146 r_free = 0.3146    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3146 r_free = 0.3146    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3146
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.0933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  17804  Z= 0.174
  Angle     :  0.555   5.434  24250  Z= 0.286
  Chirality :  0.045   0.147   2666
  Planarity :  0.005   0.063   3059
  Dihedral  :  9.696 161.809   2481
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 14.00 %
    Favored  : 85.12 %
  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: -1.56 (0.19), residues: 2073
  helix:  0.44 (0.31), residues: 312
  sheet: -1.89 (0.21), residues: 556
  loop : -0.95 (0.18), residues: 1205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 279 
 HIS   0.004   0.001   HIS C 564 
 PHE   0.010   0.001   PHE A 416 
 TYR   0.015   0.001   TYR C 509 
 ARG   0.006   0.000   ARG B 679 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04622 (  318)
  hydrogen bonds       : angle       6.80282 (  849)
  covalent geometry    : bond        0.00406 (17804)
  covalent geometry    : angle       0.55460 (24250)

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

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

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  452 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue SER  565 is missing expected H atoms. Skipping.
Evaluate side-chains
  128 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 3.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  224 LEU cc_start: 0.9111 (tp) cc_final: 0.8894 (tp)
REVERT: B  833 ILE cc_start: 0.9109 (mm) cc_final: 0.8795 (mt)
REVERT: A   49 VAL cc_start: 0.9275 (t) cc_final: 0.8882 (p)
REVERT: A   60 CYS cc_start: 0.7263 (p) cc_final: 0.7040 (p)
REVERT: A   89 LYS cc_start: 0.8719 (mtpp) cc_final: 0.8432 (mmtt)
REVERT: A  103 VAL cc_start: 0.8394 (t) cc_final: 0.8111 (t)
REVERT: A  334 ASP cc_start: 0.8619 (m-30) cc_final: 0.8412 (m-30)
REVERT: A  467 PHE cc_start: 0.7629 (m-80) cc_final: 0.7361 (m-80)
REVERT: C  369 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7597 (ttp)
REVERT: C  396 ARG cc_start: 0.8254 (mmm-85) cc_final: 0.8047 (mmm160)
REVERT: C  695 HIS cc_start: 0.5951 (t70) cc_final: 0.5543 (t-170)
REVERT: C  771 MET cc_start: 0.7205 (ttp) cc_final: 0.6886 (tmm)
  outliers start: 17
  outliers final: 11
  residues processed: 126
  average time/residue: 0.9168
  time to fit residues: 162.5859
Evaluate side-chains
  115 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 2.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 CYS
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  444 LYS
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain A residue  373 CYS
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  347 VAL
Chi-restraints excluded: chain C residue  369 MET
Chi-restraints excluded: chain C residue  773 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 209
   random chunks:
   chunk 195 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 128 optimal weight:    1.9990
   chunk 176 optimal weight:    0.4980
   chunk 110 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0870
   chunk 3 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 186 optimal weight:    2.9990
   chunk 150 optimal weight:    3.9990
   chunk 208 optimal weight:    3.9990
   overall best weight:    1.3164

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.082494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.062733 restraints weight = 151092.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 3.14
r_work: 0.3123 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3128
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  17804  Z= 0.176
  Angle     :  0.543   5.096  24250  Z= 0.280
  Chirality :  0.045   0.152   2666
  Planarity :  0.004   0.056   3059
  Dihedral  :  9.688 161.449   2477
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 14.52 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.19), residues: 2073
  helix:  0.51 (0.31), residues: 313
  sheet: -1.93 (0.21), residues: 547
  loop : -1.03 (0.18), residues: 1213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 279 
 HIS   0.003   0.001   HIS A 154 
 PHE   0.012   0.001   PHE C 742 
 TYR   0.014   0.001   TYR B 509 
 ARG   0.004   0.000   ARG C 824 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03878 (  318)
  hydrogen bonds       : angle       6.34229 (  849)
  covalent geometry    : bond        0.00413 (17804)
  covalent geometry    : angle       0.54255 (24250)

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

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

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  452 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue SER  565 is missing expected H atoms. Skipping.
Evaluate side-chains
  119 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 2.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8720 (mtpp) cc_final: 0.8424 (mmtt)
REVERT: A  103 VAL cc_start: 0.8397 (t) cc_final: 0.8114 (t)
REVERT: A  129 MET cc_start: 0.8989 (ptp) cc_final: 0.8641 (ptm)
REVERT: A  334 ASP cc_start: 0.8620 (m-30) cc_final: 0.8403 (m-30)
REVERT: A  467 PHE cc_start: 0.7662 (m-80) cc_final: 0.7385 (m-80)
REVERT: C  369 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7666 (ttp)
REVERT: C  695 HIS cc_start: 0.6027 (t70) cc_final: 0.5782 (t70)
  outliers start: 16
  outliers final: 11
  residues processed: 118
  average time/residue: 0.9174
  time to fit residues: 151.6863
Evaluate side-chains
  110 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 2.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 CYS
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  444 LYS
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  341 ILE
Chi-restraints excluded: chain C residue  347 VAL
Chi-restraints excluded: chain C residue  369 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 209
   random chunks:
   chunk 204 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 144 optimal weight:    1.9990
   chunk 151 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 104 optimal weight:    0.9980
   chunk 21 optimal weight:    0.3980
   chunk 80 optimal weight:    3.9990
   chunk 105 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.082910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.063213 restraints weight = 150904.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 3.13
r_work: 0.3137 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3142
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3142
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  17804  Z= 0.120
  Angle     :  0.516   5.811  24250  Z= 0.264
  Chirality :  0.044   0.152   2666
  Planarity :  0.004   0.063   3059
  Dihedral  :  9.578 160.909   2474
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 14.36 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.19), residues: 2073
  helix:  0.68 (0.31), residues: 312
  sheet: -1.91 (0.21), residues: 558
  loop : -0.93 (0.18), residues: 1203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 228 
 HIS   0.002   0.000   HIS A 223 
 PHE   0.011   0.001   PHE B 416 
 TYR   0.015   0.001   TYR B 509 
 ARG   0.003   0.000   ARG B 396 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03281 (  318)
  hydrogen bonds       : angle       6.07549 (  849)
  covalent geometry    : bond        0.00288 (17804)
  covalent geometry    : angle       0.51588 (24250)

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

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

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  452 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue SER  565 is missing expected H atoms. Skipping.
Evaluate side-chains
  121 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 2.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8725 (mtpp) cc_final: 0.8414 (mmtt)
REVERT: A  103 VAL cc_start: 0.8407 (t) cc_final: 0.8123 (t)
REVERT: A  129 MET cc_start: 0.8965 (ptp) cc_final: 0.8730 (ptm)
REVERT: A  334 ASP cc_start: 0.8625 (m-30) cc_final: 0.8407 (m-30)
REVERT: A  467 PHE cc_start: 0.7671 (m-80) cc_final: 0.7394 (m-80)
REVERT: C  369 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7655 (ttp)
REVERT: C  396 ARG cc_start: 0.8219 (mmm-85) cc_final: 0.8011 (mmm160)
REVERT: C  467 PHE cc_start: 0.8294 (t80) cc_final: 0.8069 (t80)
REVERT: C  695 HIS cc_start: 0.6020 (t70) cc_final: 0.5772 (t70)
  outliers start: 16
  outliers final: 10
  residues processed: 120
  average time/residue: 0.9075
  time to fit residues: 153.0670
Evaluate side-chains
  108 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 2.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 CYS
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  341 ILE
Chi-restraints excluded: chain C residue  347 VAL
Chi-restraints excluded: chain C residue  369 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 209
   random chunks:
   chunk 48 optimal weight:    0.0980
   chunk 61 optimal weight:    0.9990
   chunk 139 optimal weight:    3.9990
   chunk 125 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 119 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 148 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.082851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.063165 restraints weight = 151028.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 3.13
r_work: 0.3138 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3140
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3140
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.1496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  17804  Z= 0.118
  Angle     :  0.508   6.536  24250  Z= 0.259
  Chirality :  0.044   0.150   2666
  Planarity :  0.004   0.064   3059
  Dihedral  :  9.545 161.037   2474
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 14.31 %
    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: -1.43 (0.19), residues: 2073
  helix:  0.75 (0.31), residues: 312
  sheet: -1.85 (0.21), residues: 555
  loop : -0.90 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 228 
 HIS   0.002   0.000   HIS C 564 
 PHE   0.013   0.001   PHE C 516 
 TYR   0.021   0.001   TYR C 849 
 ARG   0.004   0.000   ARG A 735 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03088 (  318)
  hydrogen bonds       : angle       5.92879 (  849)
  covalent geometry    : bond        0.00284 (17804)
  covalent geometry    : angle       0.50753 (24250)

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

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

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  452 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue SER  565 is missing expected H atoms. Skipping.
Evaluate side-chains
  116 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 3.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8727 (mtpp) cc_final: 0.8416 (mmtt)
REVERT: A  103 VAL cc_start: 0.8399 (t) cc_final: 0.8113 (t)
REVERT: A  334 ASP cc_start: 0.8611 (m-30) cc_final: 0.8379 (m-30)
REVERT: A  467 PHE cc_start: 0.7687 (m-80) cc_final: 0.7398 (m-80)
REVERT: C  369 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7642 (ttp)
REVERT: C  396 ARG cc_start: 0.8217 (mmm-85) cc_final: 0.8011 (mmm160)
REVERT: C  467 PHE cc_start: 0.8310 (t80) cc_final: 0.8080 (t80)
REVERT: C  695 HIS cc_start: 0.6048 (t70) cc_final: 0.5804 (t70)
  outliers start: 14
  outliers final: 11
  residues processed: 115
  average time/residue: 0.9489
  time to fit residues: 153.3080
Evaluate side-chains
  111 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 2.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  444 LYS
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  489 ILE
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  347 VAL
Chi-restraints excluded: chain C residue  369 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 209
   random chunks:
   chunk 37 optimal weight:    0.0000
   chunk 169 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 156 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 166 optimal weight:    0.9980
   chunk 197 optimal weight:    3.9990
   chunk 133 optimal weight:    1.9990
   chunk 104 optimal weight:    0.5980
   chunk 102 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.082577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.062870 restraints weight = 150799.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 3.14
r_work: 0.3128 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3132
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3132
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  17804  Z= 0.135
  Angle     :  0.510   6.366  24250  Z= 0.260
  Chirality :  0.044   0.148   2666
  Planarity :  0.004   0.055   3059
  Dihedral  :  9.497 161.338   2473
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 14.15 %
    Favored  : 84.91 %
  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: -1.43 (0.19), residues: 2073
  helix:  0.81 (0.31), residues: 312
  sheet: -1.94 (0.21), residues: 568
  loop : -0.85 (0.19), residues: 1193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 228 
 HIS   0.003   0.001   HIS C 223 
 PHE   0.010   0.001   PHE B 416 
 TYR   0.019   0.001   TYR C 849 
 ARG   0.004   0.000   ARG B 396 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02979 (  318)
  hydrogen bonds       : angle       5.79425 (  849)
  covalent geometry    : bond        0.00323 (17804)
  covalent geometry    : angle       0.50988 (24250)

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

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

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  452 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue SER  565 is missing expected H atoms. Skipping.
Evaluate side-chains
  121 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 3.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   58 ARG cc_start: 0.8608 (mtp-110) cc_final: 0.8275 (mtp-110)
REVERT: A   89 LYS cc_start: 0.8728 (mtpp) cc_final: 0.8416 (mmtt)
REVERT: A  103 VAL cc_start: 0.8406 (t) cc_final: 0.8140 (t)
REVERT: A  334 ASP cc_start: 0.8599 (m-30) cc_final: 0.8377 (m-30)
REVERT: A  467 PHE cc_start: 0.7699 (m-80) cc_final: 0.7417 (m-80)
REVERT: C  369 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7650 (ttp)
REVERT: C  396 ARG cc_start: 0.8230 (mmm-85) cc_final: 0.8024 (mmm160)
REVERT: C  467 PHE cc_start: 0.8329 (t80) cc_final: 0.8109 (t80)
REVERT: C  695 HIS cc_start: 0.6006 (t70) cc_final: 0.5759 (t70)
  outliers start: 18
  outliers final: 13
  residues processed: 119
  average time/residue: 1.0137
  time to fit residues: 168.3759
Evaluate side-chains
  112 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 2.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  444 LYS
Chi-restraints excluded: chain B residue  489 ILE
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  341 ILE
Chi-restraints excluded: chain C residue  347 VAL
Chi-restraints excluded: chain C residue  369 MET
Chi-restraints excluded: chain C residue  711 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 209
   random chunks:
   chunk 207 optimal weight:    0.8980
   chunk 80 optimal weight:    3.9990
   chunk 129 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 108 optimal weight:    0.7980
   chunk 190 optimal weight:    0.9990
   chunk 121 optimal weight:    0.9980
   chunk 186 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 110 optimal weight:    0.8980
   chunk 192 optimal weight:    7.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.082540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.062828 restraints weight = 151525.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 3.14
r_work: 0.3127 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3130
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3130
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  17804  Z= 0.133
  Angle     :  0.512   5.958  24250  Z= 0.261
  Chirality :  0.044   0.172   2666
  Planarity :  0.004   0.050   3059
  Dihedral  :  9.487 161.276   2473
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 14.05 %
    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: -1.39 (0.19), residues: 2073
  helix:  0.87 (0.31), residues: 312
  sheet: -1.91 (0.21), residues: 561
  loop : -0.84 (0.19), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 228 
 HIS   0.002   0.001   HIS C 223 
 PHE   0.010   0.001   PHE B 416 
 TYR   0.017   0.001   TYR C 849 
 ARG   0.005   0.000   ARG B 396 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02950 (  318)
  hydrogen bonds       : angle       5.70190 (  849)
  covalent geometry    : bond        0.00318 (17804)
  covalent geometry    : angle       0.51153 (24250)

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

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

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  452 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue SER  565 is missing expected H atoms. Skipping.
Evaluate side-chains
  120 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 2.784 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   58 ARG cc_start: 0.8612 (mtp-110) cc_final: 0.8264 (mtp-110)
REVERT: A   89 LYS cc_start: 0.8724 (mtpp) cc_final: 0.8412 (mmtt)
REVERT: A  103 VAL cc_start: 0.8399 (t) cc_final: 0.8165 (t)
REVERT: A  334 ASP cc_start: 0.8609 (m-30) cc_final: 0.8384 (m-30)
REVERT: A  467 PHE cc_start: 0.7710 (m-80) cc_final: 0.7431 (m-80)
REVERT: C  369 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7655 (ttp)
REVERT: C  396 ARG cc_start: 0.8233 (mmm-85) cc_final: 0.8030 (mmm160)
REVERT: C  467 PHE cc_start: 0.8333 (t80) cc_final: 0.8111 (t80)
REVERT: C  695 HIS cc_start: 0.5992 (t70) cc_final: 0.5738 (t70)
  outliers start: 19
  outliers final: 13
  residues processed: 118
  average time/residue: 0.9489
  time to fit residues: 157.0117
Evaluate side-chains
  110 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 2.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  444 LYS
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  489 ILE
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  233 ASN
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  341 ILE
Chi-restraints excluded: chain C residue  347 VAL
Chi-restraints excluded: chain C residue  369 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 209
   random chunks:
   chunk 184 optimal weight:    6.9990
   chunk 79 optimal weight:    3.9990
   chunk 100 optimal weight:    0.6980
   chunk 71 optimal weight:    0.6980
   chunk 93 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 170 optimal weight:    2.9990
   chunk 195 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 111 optimal weight:    1.9990
   chunk 178 optimal weight:    2.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.082278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.062514 restraints weight = 151539.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 3.16
r_work: 0.3119 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  17804  Z= 0.145
  Angle     :  0.516   7.331  24250  Z= 0.263
  Chirality :  0.044   0.148   2666
  Planarity :  0.004   0.049   3059
  Dihedral  :  9.487 161.407   2473
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 14.41 %
    Favored  : 84.76 %
  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 (0.19), residues: 2073
  helix:  0.90 (0.31), residues: 312
  sheet: -2.00 (0.21), residues: 577
  loop : -0.81 (0.19), residues: 1184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 279 
 HIS   0.004   0.001   HIS C 223 
 PHE   0.011   0.001   PHE B 416 
 TYR   0.016   0.001   TYR C 849 
 ARG   0.004   0.000   ARG B 396 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02910 (  318)
  hydrogen bonds       : angle       5.66385 (  849)
  covalent geometry    : bond        0.00347 (17804)
  covalent geometry    : angle       0.51633 (24250)

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

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

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  452 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue SER  565 is missing expected H atoms. Skipping.
Evaluate side-chains
  117 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 2.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   58 ARG cc_start: 0.8626 (mtp-110) cc_final: 0.8334 (mtp-110)
REVERT: A  103 VAL cc_start: 0.8415 (t) cc_final: 0.8179 (t)
REVERT: A  334 ASP cc_start: 0.8601 (m-30) cc_final: 0.8374 (m-30)
REVERT: A  467 PHE cc_start: 0.7712 (m-80) cc_final: 0.7418 (m-80)
REVERT: C  369 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7684 (ttp)
REVERT: C  467 PHE cc_start: 0.8342 (t80) cc_final: 0.8118 (t80)
REVERT: C  695 HIS cc_start: 0.6060 (t70) cc_final: 0.5796 (t70)
  outliers start: 16
  outliers final: 13
  residues processed: 116
  average time/residue: 0.8891
  time to fit residues: 145.0192
Evaluate side-chains
  113 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 2.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  444 LYS
Chi-restraints excluded: chain B residue  489 ILE
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  233 ASN
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  341 ILE
Chi-restraints excluded: chain C residue  347 VAL
Chi-restraints excluded: chain C residue  369 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 209
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   chunk 50 optimal weight:    0.0980
   chunk 135 optimal weight:    1.9990
   chunk 158 optimal weight:    1.9990
   chunk 132 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 163 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
C 105 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.082144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.062615 restraints weight = 150734.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 3.07
r_work: 0.3127 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3130
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3130
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  17804  Z= 0.136
  Angle     :  0.512   6.047  24250  Z= 0.260
  Chirality :  0.044   0.149   2666
  Planarity :  0.004   0.048   3059
  Dihedral  :  9.482 161.284   2473
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 14.36 %
    Favored  : 84.86 %
  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: -1.35 (0.19), residues: 2073
  helix:  0.92 (0.31), residues: 312
  sheet: -1.92 (0.21), residues: 562
  loop : -0.80 (0.19), residues: 1199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 228 
 HIS   0.003   0.001   HIS C 223 
 PHE   0.011   0.001   PHE B 416 
 TYR   0.016   0.001   TYR C 849 
 ARG   0.004   0.000   ARG B 396 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02838 (  318)
  hydrogen bonds       : angle       5.58821 (  849)
  covalent geometry    : bond        0.00327 (17804)
  covalent geometry    : angle       0.51161 (24250)

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

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

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  452 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue SER  565 is missing expected H atoms. Skipping.
Evaluate side-chains
  115 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 3.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   58 ARG cc_start: 0.8625 (mtp-110) cc_final: 0.8378 (mtp-110)
REVERT: A  103 VAL cc_start: 0.8421 (t) cc_final: 0.8184 (t)
REVERT: A  334 ASP cc_start: 0.8596 (m-30) cc_final: 0.8364 (m-30)
REVERT: A  467 PHE cc_start: 0.7710 (m-80) cc_final: 0.7417 (m-80)
REVERT: C  369 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7686 (ttp)
REVERT: C  467 PHE cc_start: 0.8331 (t80) cc_final: 0.8105 (t80)
REVERT: C  695 HIS cc_start: 0.6111 (t70) cc_final: 0.5846 (t70)
  outliers start: 15
  outliers final: 13
  residues processed: 114
  average time/residue: 1.0162
  time to fit residues: 164.5436
Evaluate side-chains
  112 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 2.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  444 LYS
Chi-restraints excluded: chain B residue  489 ILE
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  233 ASN
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  341 ILE
Chi-restraints excluded: chain C residue  347 VAL
Chi-restraints excluded: chain C residue  369 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 209
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 35 optimal weight:    0.3980
   chunk 69 optimal weight:    1.9990
   chunk 191 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 21 optimal weight:    0.1980
   chunk 179 optimal weight:    1.9990
   chunk 180 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0170
   chunk 143 optimal weight:    0.0670
   chunk 80 optimal weight:    3.9990
   overall best weight:    0.2956

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

Flipped N/Q/H residues before XYZ refinement:
C 451 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.083022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.063596 restraints weight = 149698.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 3.09
r_work: 0.3151 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3153
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3153
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  17804  Z= 0.089
  Angle     :  0.496   6.598  24250  Z= 0.251
  Chirality :  0.044   0.153   2666
  Planarity :  0.004   0.069   3059
  Dihedral  :  9.396 160.786   2473
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 14.72 %
    Favored  : 84.76 %
  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: -1.25 (0.19), residues: 2073
  helix:  1.07 (0.31), residues: 312
  sheet: -1.92 (0.21), residues: 579
  loop : -0.68 (0.19), residues: 1182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 228 
 HIS   0.002   0.000   HIS C 223 
 PHE   0.010   0.001   PHE B 416 
 TYR   0.015   0.001   TYR C 849 
 ARG   0.011   0.000   ARG B 490 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02569 (  318)
  hydrogen bonds       : angle       5.38365 (  849)
  covalent geometry    : bond        0.00221 (17804)
  covalent geometry    : angle       0.49556 (24250)

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

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

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4146 Ramachandran restraints generated.
    2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  452 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue SER  565 is missing expected H atoms. Skipping.
Evaluate side-chains
  112 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 3.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 VAL cc_start: 0.8408 (t) cc_final: 0.8168 (t)
REVERT: A  129 MET cc_start: 0.8875 (ptp) cc_final: 0.8545 (ptm)
REVERT: A  334 ASP cc_start: 0.8603 (m-30) cc_final: 0.8385 (m-30)
REVERT: A  467 PHE cc_start: 0.7713 (m-80) cc_final: 0.7413 (m-80)
REVERT: C  176 LYS cc_start: 0.8452 (mmmt) cc_final: 0.7944 (mmtt)
REVERT: C  369 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7656 (ttp)
REVERT: C  467 PHE cc_start: 0.8319 (t80) cc_final: 0.8090 (t80)
REVERT: C  695 HIS cc_start: 0.6095 (t70) cc_final: 0.5837 (t70)
  outliers start: 10
  outliers final: 8
  residues processed: 111
  average time/residue: 0.9023
  time to fit residues: 141.5863
Evaluate side-chains
  110 residues out of total 1934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 3.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  489 ILE
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  341 ILE
Chi-restraints excluded: chain C residue  347 VAL
Chi-restraints excluded: chain C residue  369 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 209
   random chunks:
   chunk 127 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0370
   chunk 35 optimal weight:    0.7980
   chunk 71 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 123 optimal weight:    0.5980
   chunk 110 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0870
   chunk 67 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.4436

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

Flipped N/Q/H residues before XYZ refinement:
B 312 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.082973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.063556 restraints weight = 150449.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 3.08
r_work: 0.3150 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3152
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3152
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  17804  Z= 0.095
  Angle     :  0.494   6.186  24250  Z= 0.250
  Chirality :  0.044   0.150   2666
  Planarity :  0.004   0.054   3059
  Dihedral  :  9.369 161.219   2473
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.53 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 14.88 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.17 (0.19), residues: 2073
  helix:  1.13 (0.31), residues: 312
  sheet: -1.83 (0.21), residues: 565
  loop : -0.67 (0.19), residues: 1196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 228 
 HIS   0.002   0.000   HIS C 223 
 PHE   0.008   0.001   PHE B 416 
 TYR   0.016   0.001   TYR C 849 
 ARG   0.007   0.000   ARG B 490 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02552 (  318)
  hydrogen bonds       : angle       5.33693 (  849)
  covalent geometry    : bond        0.00237 (17804)
  covalent geometry    : angle       0.49366 (24250)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 18861.77 seconds
wall clock time: 320 minutes 20.00 seconds (19220.00 seconds total)