Starting phenix.real_space_refine
on Sat Jul  4 01:51:19 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8dmg_27536/07_2026/8dmg_27536.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dmg_27536/07_2026/8dmg_27536.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dmg_27536/07_2026/8dmg_27536.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dmg_27536/07_2026/8dmg_27536.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dmg_27536/07_2026/8dmg_27536.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dmg_27536/07_2026/8dmg_27536.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8dmg_27536/07_2026/8dmg_27536.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8dmg_27536/07_2026/8dmg_27536.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.128
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Fe      2      7.16       5
     P       6      5.49       5
     S      78      5.16       5
     C   10544      2.51       5
     N    2812      2.21       5
     O    3200      1.98       5
     H     202      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.19s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 16844
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8236
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1034, 8200
          Classifications: {'peptide': 1034}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 54, 'TRANS': 979}
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 100
          Unresolved non-hydrogen angles: 120
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 13, 'GLN:plan1': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 59
      Conformer: "B"
        Number of residues, atoms: 1034, 8200
          Classifications: {'peptide': 1034}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 54, 'TRANS': 979}
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 100
          Unresolved non-hydrogen angles: 120
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 13, 'GLN:plan1': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 59
          bond proxies already assigned to first conformer: 8341
    Chain: "B"
      Number of atoms: 8238
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1034, 8202
          Classifications: {'peptide': 1034}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 54, 'TRANS': 979}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 98
          Unresolved non-hydrogen angles: 118
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 13, 'GLN:plan1': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 59
      Conformer: "B"
        Number of residues, atoms: 1034, 8202
          Classifications: {'peptide': 1034}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 54, 'TRANS': 979}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 98
          Unresolved non-hydrogen angles: 118
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 13, 'GLN:plan1': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 59
          bond proxies already assigned to first conformer: 8342
    Chain: "A"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 185
          Unusual residues: {'1C6': 1, 'FAD': 1, 'FMN': 1, 'HEM': 1, 'PG4': 2, 'SO4': 3}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 185
          Unusual residues: {'1C6': 1, 'FAD': 1, 'FMN': 1, 'HEM': 1, 'PG4': 2, 'SO4': 3}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   3247  SG  CYS A 400      53.201  45.582 102.548  1.00 11.59           S
  ATOM  11483  SG  CYS B 400      38.400  45.550  47.133  1.00 11.59           S

  Residues with excluded nonbonded symmetry interactions: 8
    residue:
      pdb=" N  APHE A  87 " occ=0.20
      ... (20 atoms not shown)
      pdb=" CZ BPHE A  87 " occ=0.20
    residue:
      pdb=" N  AASP A 168 " occ=0.20
      ... (14 atoms not shown)
      pdb=" OD2BASP A 168 " occ=0.20
    residue:
      pdb=" N  AASP A 182 " occ=0.20
      ... (14 atoms not shown)
      pdb=" OD2BASP A 182 " occ=0.20
    residue:
      pdb=" N  AGLN A 310 " occ=0.20
      ... (16 atoms not shown)
      pdb=" NE2BGLN A 310 " occ=0.20
    residue:
      pdb=" N  APHE B  87 " occ=0.20
      ... (20 atoms not shown)
      pdb=" CZ BPHE B  87 " occ=0.20
    residue:
      pdb=" N  AASP B 168 " occ=0.20
      ... (14 atoms not shown)
      pdb=" OD2BASP B 168 " occ=0.20
    residue:
      pdb=" N  AASP B 182 " occ=0.20
      ... (14 atoms not shown)
      pdb=" OD2BASP B 182 " occ=0.20
    residue:
      pdb=" N  AGLN B 310 " occ=0.20
      ... (16 atoms not shown)
      pdb=" NE2BGLN B 310 " occ=0.20
  Time building chain proxies: 6.43, per 1000 atoms: 0.38
  Number of scatterers: 16844
  At special positions: 0
  Unit cell: (96.96, 133.32, 153.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Fe      2     26.01
     S      78     16.00
     P       6     15.00
     O    3200      8.00
     N    2812      7.00
     C   10544      6.00
     H     202      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=7, symmetry=0
  Number of additional bonds: simple=7, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.62
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3908

  Finding SS restraints...
    Secondary structure from input PDB file:
      97 helices and 18 sheets defined
      51.0% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 15
    Processing helix  chain 'A' and resid 16 through 21
    Processing helix  chain 'A' and resid 24 through 37
    Processing helix  chain 'A' and resid 54 through 62
      removed outlier: 4.256A  pdb=" N   GLU A  60 " --> pdb=" O   ARG A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 83
      removed outlier: 3.899A  pdb=" N   ASP A  80 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   PHE A  81 " --> pdb=" O   PHE A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 104
      removed outlier: 4.065A  pdb=" N   LYS A  97 " --> pdb=" O   GLU A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 107
      No H-bonds generated for 'chain 'A' and resid 105 through 107'
    Processing helix  chain 'A' and resid 108 through 132
      removed outlier: 4.760A  pdb=" N   ALA A 117 " --> pdb=" O   LYS A 113 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   MET A 118 " --> pdb=" O   GLY A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 159
    Processing helix  chain 'A' and resid 163 through 167
    Processing helix  chain 'A' and resid 171 through 188
      removed outlier: 3.650A  pdb=" N   LEU A 188 " --> pdb=" O   ALA A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 197
      No H-bonds generated for 'chain 'A' and resid 195 through 197'
    Processing helix  chain 'A' and resid 198 through 226
    Processing helix  chain 'A' and resid 232 through 240
    Processing helix  chain 'A' and resid 250 through 265
    Processing helix  chain 'A' and resid 266 through 283
    Processing helix  chain 'A' and resid 283 through 298
    Processing helix  chain 'A' and resid 304 through 311
    Processing helix  chain 'A' and resid 311 through 325
    Processing helix  chain 'A' and resid 357 through 361
    Processing helix  chain 'A' and resid 363 through 368
    Processing helix  chain 'A' and resid 375 through 380
    Processing helix  chain 'A' and resid 381 through 385
    Processing helix  chain 'A' and resid 395 through 399
    Processing helix  chain 'A' and resid 402 through 420
    Processing helix  chain 'A' and resid 491 through 506
      removed outlier: 3.553A  pdb=" N   SER A 506 " --> pdb=" O   ASP A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 519
      No H-bonds generated for 'chain 'A' and resid 517 through 519'
    Processing helix  chain 'A' and resid 544 through 553
    Processing helix  chain 'A' and resid 574 through 578
      removed outlier: 3.783A  pdb=" N   TYR A 578 " --> pdb=" O   ALA A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 591
    Processing helix  chain 'A' and resid 608 through 628
    Processing helix  chain 'A' and resid 653 through 659
    Processing helix  chain 'A' and resid 707 through 719
    Processing helix  chain 'A' and resid 746 through 750
    Processing helix  chain 'A' and resid 751 through 753
      No H-bonds generated for 'chain 'A' and resid 751 through 753'
    Processing helix  chain 'A' and resid 760 through 770
    Processing helix  chain 'A' and resid 773 through 783
    Processing helix  chain 'A' and resid 785 through 793
    Processing helix  chain 'A' and resid 799 through 807
    Processing helix  chain 'A' and resid 813 through 820
      removed outlier: 3.611A  pdb=" N   ALA A 819 " --> pdb=" O   SER A 815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 871
    Processing helix  chain 'A' and resid 903 through 905
      No H-bonds generated for 'chain 'A' and resid 903 through 905'
    Processing helix  chain 'A' and resid 906 through 923
      removed outlier: 4.702A  pdb=" N   PHE A 910 " --> pdb=" O   GLY A 906 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLY A 912 " --> pdb=" O   ALA A 908 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 945 through 955
    Processing helix  chain 'A' and resid 974 through 982
    Processing helix  chain 'A' and resid 982 through 992
    Processing helix  chain 'A' and resid 1004 through 1021
    Processing helix  chain 'A' and resid 1024 through 1036
    Processing helix  chain 'B' and resid 11 through 15
    Processing helix  chain 'B' and resid 16 through 21
    Processing helix  chain 'B' and resid 24 through 37
    Processing helix  chain 'B' and resid 54 through 62
      removed outlier: 4.256A  pdb=" N   GLU B  60 " --> pdb=" O   ARG B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 83
      removed outlier: 3.899A  pdb=" N   ASP B  80 " --> pdb=" O   LYS B  76 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   PHE B  81 " --> pdb=" O   PHE B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 104
      removed outlier: 4.065A  pdb=" N   LYS B  97 " --> pdb=" O   GLU B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 107
      No H-bonds generated for 'chain 'B' and resid 105 through 107'
    Processing helix  chain 'B' and resid 108 through 132
      removed outlier: 4.760A  pdb=" N   ALA B 117 " --> pdb=" O   LYS B 113 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   MET B 118 " --> pdb=" O   GLY B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 159
    Processing helix  chain 'B' and resid 163 through 167
    Processing helix  chain 'B' and resid 171 through 188
      removed outlier: 3.650A  pdb=" N   LEU B 188 " --> pdb=" O   ALA B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 197
      No H-bonds generated for 'chain 'B' and resid 195 through 197'
    Processing helix  chain 'B' and resid 198 through 226
    Processing helix  chain 'B' and resid 232 through 240
    Processing helix  chain 'B' and resid 250 through 265
    Processing helix  chain 'B' and resid 266 through 283
    Processing helix  chain 'B' and resid 283 through 298
    Processing helix  chain 'B' and resid 304 through 311
    Processing helix  chain 'B' and resid 311 through 325
    Processing helix  chain 'B' and resid 357 through 361
    Processing helix  chain 'B' and resid 363 through 368
    Processing helix  chain 'B' and resid 375 through 380
    Processing helix  chain 'B' and resid 381 through 385
    Processing helix  chain 'B' and resid 395 through 399
    Processing helix  chain 'B' and resid 402 through 420
    Processing helix  chain 'B' and resid 491 through 506
      removed outlier: 3.554A  pdb=" N   SER B 506 " --> pdb=" O   ASP B 502 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 517 through 519
      No H-bonds generated for 'chain 'B' and resid 517 through 519'
    Processing helix  chain 'B' and resid 544 through 553
    Processing helix  chain 'B' and resid 574 through 578
      removed outlier: 3.784A  pdb=" N   TYR B 578 " --> pdb=" O   ALA B 575 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 579 through 591
    Processing helix  chain 'B' and resid 608 through 628
    Processing helix  chain 'B' and resid 634 through 638
      removed outlier: 3.526A  pdb=" N   ASP B 637 " --> pdb=" O   ASN B 634 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 653 through 659
    Processing helix  chain 'B' and resid 707 through 719
    Processing helix  chain 'B' and resid 746 through 750
    Processing helix  chain 'B' and resid 751 through 753
      No H-bonds generated for 'chain 'B' and resid 751 through 753'
    Processing helix  chain 'B' and resid 760 through 770
    Processing helix  chain 'B' and resid 773 through 783
    Processing helix  chain 'B' and resid 785 through 793
    Processing helix  chain 'B' and resid 799 through 807
    Processing helix  chain 'B' and resid 813 through 820
      removed outlier: 3.611A  pdb=" N   ALA B 819 " --> pdb=" O   SER B 815 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 862 through 871
    Processing helix  chain 'B' and resid 903 through 905
      No H-bonds generated for 'chain 'B' and resid 903 through 905'
    Processing helix  chain 'B' and resid 906 through 923
      removed outlier: 4.703A  pdb=" N   PHE B 910 " --> pdb=" O   GLY B 906 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLY B 912 " --> pdb=" O   ALA B 908 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 945 through 955
    Processing helix  chain 'B' and resid 974 through 982
    Processing helix  chain 'B' and resid 982 through 992
    Processing helix  chain 'B' and resid 1004 through 1021
    Processing helix  chain 'B' and resid 1024 through 1036
    Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 44
      removed outlier: 4.840A  pdb=" N   GLU A 352 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   SER A 332 " --> pdb=" O   ASN A  70 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 139 through 140
    Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 341
    Processing sheet with id=AA4, first strand: chain 'A' and resid 433 through 435
    Processing sheet with id=AA5, first strand: chain 'A' and resid 512 through 515
      removed outlier: 6.476A  pdb=" N   LEU A 483 " --> pdb=" O   LEU A 530 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   VAL A 532 " --> pdb=" O   LEU A 483 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   LEU A 485 " --> pdb=" O   VAL A 532 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   VAL A 529 " --> pdb=" O   SER A 565 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   PHE A 567 " --> pdb=" O   VAL A 529 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   ILE A 531 " --> pdb=" O   PHE A 567 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   CYS A 569 " --> pdb=" O   ILE A 531 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   THR A 533 " --> pdb=" O   CYS A 569 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ASP A 599 " --> pdb=" O   TYR A 564 " (cutoff:3.500A)
      removed outlier: 5.354A  pdb=" N   VAL A 566 " --> pdb=" O   ASP A 599 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 827 through 830
      removed outlier: 4.840A  pdb=" N   THR A 878 " --> pdb=" O   ILE A 703 " (cutoff:3.500A)
      removed outlier: 4.701A  pdb=" N   ASN A 665 " --> pdb=" O   GLU A 687 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   GLU A 685 " --> pdb=" O   VAL A 667 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   SER A 669 " --> pdb=" O   HIS A 683 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   HIS A 683 " --> pdb=" O   SER A 669 " (cutoff:3.500A)
      removed outlier: 5.070A  pdb=" N   GLU A 671 " --> pdb=" O   THR A 681 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   THR A 681 " --> pdb=" O   GLU A 671 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 743 through 745
      removed outlier: 3.586A  pdb=" N   LEU A 728 " --> pdb=" O   GLN B 645 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLN B 645 " --> pdb=" O   LEU A 728 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 850 through 852
    Processing sheet with id=AA9, first strand: chain 'A' and resid 959 through 964
      removed outlier: 6.368A  pdb=" N   ALA A 930 " --> pdb=" O   THR A 959 " (cutoff:3.500A)
      removed outlier: 7.458A  pdb=" N   HIS A 961 " --> pdb=" O   ALA A 930 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   LEU A 932 " --> pdb=" O   HIS A 961 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   ALA A 963 " --> pdb=" O   LEU A 932 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   PHE A 934 " --> pdb=" O   ALA A 963 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   LEU A 898 " --> pdb=" O   HIS A 931 " (cutoff:3.500A)
      removed outlier: 8.028A  pdb=" N   TYR A 933 " --> pdb=" O   LEU A 898 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   MET A 900 " --> pdb=" O   TYR A 933 " (cutoff:3.500A)
      removed outlier: 8.313A  pdb=" N   GLY A 935 " --> pdb=" O   MET A 900 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 39 through 44
      removed outlier: 4.840A  pdb=" N   GLU B 352 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   SER B 332 " --> pdb=" O   ASN B  70 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 139 through 140
    Processing sheet with id=AB3, first strand: chain 'B' and resid 339 through 341
    Processing sheet with id=AB4, first strand: chain 'B' and resid 433 through 435
    Processing sheet with id=AB5, first strand: chain 'B' and resid 512 through 515
      removed outlier: 6.475A  pdb=" N   LEU B 483 " --> pdb=" O   LEU B 530 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   VAL B 532 " --> pdb=" O   LEU B 483 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   LEU B 485 " --> pdb=" O   VAL B 532 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   VAL B 529 " --> pdb=" O   SER B 565 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   PHE B 567 " --> pdb=" O   VAL B 529 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   ILE B 531 " --> pdb=" O   PHE B 567 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   CYS B 569 " --> pdb=" O   ILE B 531 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   THR B 533 " --> pdb=" O   CYS B 569 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ASP B 599 " --> pdb=" O   TYR B 564 " (cutoff:3.500A)
      removed outlier: 5.353A  pdb=" N   VAL B 566 " --> pdb=" O   ASP B 599 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 827 through 830
      removed outlier: 4.841A  pdb=" N   THR B 878 " --> pdb=" O   ILE B 703 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   ASN B 665 " --> pdb=" O   GLU B 687 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   GLU B 685 " --> pdb=" O   VAL B 667 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   SER B 669 " --> pdb=" O   HIS B 683 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   HIS B 683 " --> pdb=" O   SER B 669 " (cutoff:3.500A)
      removed outlier: 5.070A  pdb=" N   GLU B 671 " --> pdb=" O   THR B 681 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   THR B 681 " --> pdb=" O   GLU B 671 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 725 through 727
    Processing sheet with id=AB8, first strand: chain 'B' and resid 850 through 852
    Processing sheet with id=AB9, first strand: chain 'B' and resid 959 through 964
      removed outlier: 6.367A  pdb=" N   ALA B 930 " --> pdb=" O   THR B 959 " (cutoff:3.500A)
      removed outlier: 7.456A  pdb=" N   HIS B 961 " --> pdb=" O   ALA B 930 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   LEU B 932 " --> pdb=" O   HIS B 961 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   ALA B 963 " --> pdb=" O   LEU B 932 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   PHE B 934 " --> pdb=" O   ALA B 963 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   LEU B 898 " --> pdb=" O   HIS B 931 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   TYR B 933 " --> pdb=" O   LEU B 898 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   MET B 900 " --> pdb=" O   TYR B 933 " (cutoff:3.500A)
      removed outlier: 8.313A  pdb=" N   GLY B 935 " --> pdb=" O   MET B 900 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   ILE B 899 " --> pdb=" O   TYR B 997 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N   CYS B 999 " --> pdb=" O   ILE B 899 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   VAL B 901 " --> pdb=" O   CYS B 999 " (cutoff:3.500A)
      removed outlier: 7.522A  pdb=" N   ASP B1001 " --> pdb=" O   VAL B 901 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   PHE B 996 " --> pdb=" O   ALA B1042 " (cutoff:3.500A)
      removed outlier: 8.165A  pdb=" N   ASP B1044 " --> pdb=" O   PHE B 996 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   ILE B 998 " --> pdb=" O   ASP B1044 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   TRP B1046 " --> pdb=" O   ILE B 998 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   GLY B1000 " --> pdb=" O   TRP B1046 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9

    800 hydrogen bonds defined for protein.
    2263 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: 3.18

  Time building geometry restraints manager: 2.03 seconds

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

  Histogram of bond lengths:
        0.82 -     1.23: 1569
        1.23 -     1.65: 15523
        1.65 -     2.06: 143
        2.06 -     2.48: 2
        2.48 -     2.89: 2
  Bond restraints: 17239
  Sorted by residual:
  bond pdb=" C   HIS A 478 "
       pdb=" N   ASN A 479 "
    ideal  model  delta    sigma   weight residual
    1.332  2.890 -1.558 1.40e-02 5.10e+03 1.24e+04
  bond pdb=" C   LEU B 630 "
       pdb=" N   ASP B 631 "
    ideal  model  delta    sigma   weight residual
    1.333  2.502 -1.169 1.50e-02 4.44e+03 6.08e+03
  bond pdb=" C   ALA A 661 "
       pdb=" N   PHE A 662 "
    ideal  model  delta    sigma   weight residual
    1.330  0.856  0.473 1.37e-02 5.33e+03 1.19e+03
  bond pdb=" C   ALA B 661 "
       pdb=" N   PHE B 662 "
    ideal  model  delta    sigma   weight residual
    1.330  0.856  0.473 1.37e-02 5.33e+03 1.19e+03
  bond pdb=" N   PRO A 774 "
       pdb=" CD  PRO A 774 "
    ideal  model  delta    sigma   weight residual
    1.473  1.682 -0.209 1.40e-02 5.10e+03 2.23e+02
  ... (remaining 17234 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    11.64: 23554
       11.64 -    23.28: 49
       23.28 -    34.93: 8
       34.93 -    46.57: 7
       46.57 -    58.21: 3
  Bond angle restraints: 23621
  Sorted by residual:
  angle pdb=" CA  HIS A 478 "
        pdb=" C   HIS A 478 "
        pdb=" N   ASN A 479 "
      ideal   model   delta    sigma   weight residual
     116.25   65.98   50.27 1.53e+00 4.27e-01 1.08e+03
  angle pdb=" O   LEU B 630 "
        pdb=" C   LEU B 630 "
        pdb=" N   ASP B 631 "
      ideal   model   delta    sigma   weight residual
     123.28   85.84   37.44 1.16e+00 7.43e-01 1.04e+03
  angle pdb=" N   ALA B 736 "
        pdb=" CA  ALA B 736 "
        pdb=" CB  ALA B 736 "
      ideal   model   delta    sigma   weight residual
     109.51  151.10  -41.59 1.58e+00 4.01e-01 6.93e+02
  angle pdb=" N   ALA A 736 "
        pdb=" CA  ALA A 736 "
        pdb=" CB  ALA A 736 "
      ideal   model   delta    sigma   weight residual
     109.51  151.10  -41.59 1.58e+00 4.01e-01 6.93e+02
  angle pdb=" N   LYS B 734 "
        pdb=" CA  LYS B 734 "
        pdb=" CB  LYS B 734 "
      ideal   model   delta    sigma   weight residual
     111.74   71.30   40.44 1.69e+00 3.50e-01 5.73e+02
  ... (remaining 23616 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.26: 9214
       20.26 -    40.52: 721
       40.52 -    60.79: 219
       60.79 -    81.05: 44
       81.05 -   101.31: 13
  Dihedral angle restraints: 10211
    sinusoidal: 4146
      harmonic: 6065
  Sorted by residual:
  dihedral pdb=" N   LYS B 734 "
           pdb=" C   LYS B 734 "
           pdb=" CA  LYS B 734 "
           pdb=" CB  LYS B 734 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80   78.24   44.56     0      2.50e+00 1.60e-01 3.18e+02
  dihedral pdb=" N   LYS A 734 "
           pdb=" C   LYS A 734 "
           pdb=" CA  LYS A 734 "
           pdb=" CB  LYS A 734 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80   78.25   44.55     0      2.50e+00 1.60e-01 3.18e+02
  dihedral pdb=" N   ALA A 736 "
           pdb=" C   ALA A 736 "
           pdb=" CA  ALA A 736 "
           pdb=" CB  ALA A 736 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.90  156.51  -33.61     0      2.50e+00 1.60e-01 1.81e+02
  ... (remaining 10208 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.228: 2370
       0.228 -    0.456: 99
       0.456 -    0.683: 10
       0.683 -    0.911: 0
       0.911 -    1.139: 5
  Chirality restraints: 2484
  Sorted by residual:
  chirality pdb=" CA  ALA A 736 "
            pdb=" N   ALA A 736 "
            pdb=" C   ALA A 736 "
            pdb=" CB  ALA A 736 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.35    1.14 2.00e-01 2.50e+01 3.24e+01
  chirality pdb=" CA  ALA B 736 "
            pdb=" N   ALA B 736 "
            pdb=" C   ALA B 736 "
            pdb=" CB  ALA B 736 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.35    1.13 2.00e-01 2.50e+01 3.22e+01
  chirality pdb=" CA  HIS B 478 "
            pdb=" N   HIS B 478 "
            pdb=" C   HIS B 478 "
            pdb=" CB  HIS B 478 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.50    1.01 2.00e-01 2.50e+01 2.54e+01
  ... (remaining 2481 not shown)

  Planarity restraints: 3023
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 630 "    0.188 2.00e-02 2.50e+03   2.74e-01 7.49e+02
        pdb=" C   LEU B 630 "   -0.452 2.00e-02 2.50e+03
        pdb=" O   LEU B 630 "    0.245 2.00e-02 2.50e+03
        pdb=" N   ASP B 631 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 478 "   -0.179 2.00e-02 2.50e+03   2.28e-01 5.19e+02
        pdb=" C   HIS A 478 "    0.349 2.00e-02 2.50e+03
        pdb=" O   HIS A 478 "   -0.225 2.00e-02 2.50e+03
        pdb=" N   ASN A 479 "    0.055 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' FMN B1103 "    0.007 2.00e-02 2.50e+03   6.83e-02 2.21e+02
        pdb=" C10 FMN B1103 "    0.107 2.00e-02 2.50e+03
        pdb=" C2  FMN B1103 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4  FMN B1103 "   -0.055 2.00e-02 2.50e+03
        pdb=" C4A FMN B1103 "    0.108 2.00e-02 2.50e+03
        pdb=" C5A FMN B1103 "    0.007 2.00e-02 2.50e+03
        pdb=" C6  FMN B1103 "    0.053 2.00e-02 2.50e+03
        pdb=" C7  FMN B1103 "    0.020 2.00e-02 2.50e+03
        pdb=" C7M FMN B1103 "    0.052 2.00e-02 2.50e+03
        pdb=" C8  FMN B1103 "   -0.053 2.00e-02 2.50e+03
        pdb=" C8M FMN B1103 "   -0.101 2.00e-02 2.50e+03
        pdb=" C9  FMN B1103 "   -0.053 2.00e-02 2.50e+03
        pdb=" C9A FMN B1103 "   -0.028 2.00e-02 2.50e+03
        pdb=" N1  FMN B1103 "    0.097 2.00e-02 2.50e+03
        pdb=" N10 FMN B1103 "   -0.007 2.00e-02 2.50e+03
        pdb=" N3  FMN B1103 "   -0.086 2.00e-02 2.50e+03
        pdb=" N5  FMN B1103 "    0.086 2.00e-02 2.50e+03
        pdb=" O2  FMN B1103 "   -0.031 2.00e-02 2.50e+03
        pdb=" O4  FMN B1103 "   -0.121 2.00e-02 2.50e+03
  ... (remaining 3020 not shown)

  Histogram of nonbonded interaction distances:
        0.31 -     1.17: 5
        1.17 -     2.03: 77
        2.03 -     2.88: 7673
        2.88 -     3.74: 36575
        3.74 -     4.60: 69867
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 114197
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 732 "
            pdb=" O   THR B 641 "
     model   vdw
     0.312 2.800
  nonbonded pdb=" CG  ASN A 381 "
            pdb=" OE1 GLN B 546 "
     model   vdw
     0.380 3.100
  nonbonded pdb=" O   THR A 641 "
            pdb=" OE1 GLU B 732 "
     model   vdw
     0.707 2.800
  nonbonded pdb=" NE2 GLN A 546 "
            pdb=" ND2 ASN B 381 "
     model   vdw
     0.898 3.100
  nonbonded pdb=" OE1 GLU A 732 "
            pdb=" C   THR B 641 "
     model   vdw
     1.055 3.100
  ... (remaining 114192 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 3 through 86 or resid 88 through 167 or resid 169 through  \ 
181 or resid 183 through 309 or resid 311 through 1109))
  selection = (chain 'B' and (resid 3 through 86 or resid 88 through 167 or resid 169 through  \ 
181 or resid 183 through 309 or resid 311 through 1040 or (resid 1041 and (name  \ 
N or name CA or name C or name CB or name CG or name CD1 or name CD2 or name CE1 \ 
 or name CE2 or name CZ or name OH )) or resid 1042 through 1043 or (resid 1044  \ 
and (name N or name CA or name C or name CB or name CG or name OD1 or name OD2)) \ 
 or resid 1045 through 1109))
}

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=0.20 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.170
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     19.730
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6079
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      :  0.030   1.558  17044  Z= 2.019
  Angle     :  2.330  58.209  23153  Z= 1.418
  Chirality :  0.122   1.139   2484
  Planarity :  0.014   0.274   2995
  Dihedral  : 16.890 101.311   6237
  Min Nonbonded Distance : 0.312

Molprobity Statistics.
  All-atom Clashscore : 28.62
  Ramachandran Plot:
    Outliers :  1.65 %
    Allowed  :  6.03 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  6.80 %
    Allowed  :  6.68 %
    Favored  : 86.52 %
  Cbeta Deviations :  1.02 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.43 (0.16), residues: 2082
  helix: -1.76 (0.13), residues: 944
  sheet: -0.76 (0.30), residues: 277
  loop : -1.54 (0.20), residues: 861

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.038   0.003   ARG B 398 
 TYR   0.047   0.010   TYR B 694 
 PHE   0.054   0.010   PHE A 107 
 TRP   0.087   0.012   TRP B  96 
 HIS   0.030   0.007   HIS A  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.02866 /  1.79 (17037)
  covalent geometry    : angle       2.32968 /  1.42 (23153)
  hydrogen bonds       : bond        0.18694 / 12.27 (  800)
  hydrogen bonds       : angle       8.05440 /  5.71 ( 2263)
  Misc. bond           : bond        0.46388 / 24.76 (    7)

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

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

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  362 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 116
    poor density    : 246
  time to evaluate  : 0.654 
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
TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it.
   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: symmetry clash
   revert: symmetry clash
REVERT: A  150 LEU cc_start: 0.7743 (tp) cc_final: 0.7528 (tp)
REVERT: A  177 MET cc_start: 0.7413 (ttp) cc_final: 0.6764 (tmm)
REVERT: A  272 LEU cc_start: 0.7757 (tp) cc_final: 0.7484 (tt)
REVERT: A  314 VAL cc_start: 0.8500 (t) cc_final: 0.7885 (t)
REVERT: A  357 ILE cc_start: 0.7172 (mt) cc_final: 0.6783 (mm)
REVERT: A  411 THR cc_start: 0.8551 (m) cc_final: 0.7868 (t)
REVERT: A  644 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6441 (pt)
REVERT: A  913 PHE cc_start: 0.6518 (m-10) cc_final: 0.5979 (m-10)
REVERT: A 1016 SER cc_start: 0.7616 (m) cc_final: 0.6906 (t)
REVERT: B   62 CYS cc_start: 0.2999 (m) cc_final: 0.2573 (m)
REVERT: B  216 VAL cc_start: 0.8727 (t) cc_final: 0.8396 (t)
REVERT: B  471 ARG cc_start: 0.6184 (OUTLIER) cc_final: 0.5463 (ptt180)
REVERT: B  629 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.6984 (p0)
REVERT: B  659 HIS cc_start: 0.6522 (m-70) cc_final: 0.6020 (m-70)
REVERT: B  793 VAL cc_start: 0.5659 (t) cc_final: 0.5063 (t)
REVERT: B  847 SER cc_start: 0.6713 (OUTLIER) cc_final: 0.6097 (p)
  outliers start: 116
  outliers final: 33
  residues processed: 343
  average time/residue: 0.1303
  time to fit residues: 66.9627
Evaluate side-chains
  179 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 142
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 194 optimal weight:    4.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.8980
   chunk 200 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    5.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  27 GLN
A  73 GLN
A  95 ASN
A 134 ASN
A 201 ASN
A 236 HIS
** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 283 ASN
** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 403 GLN
A 645 GLN
A 923 GLN
A 951 ASN
A 992 GLN
B  16 ASN
B  73 GLN
B 134 ASN
B 201 ASN
B 236 HIS
B 253 ASN
B 283 ASN
B 388 HIS
B 403 GLN
B 645 GLN
B 699 HIS
B 923 GLN
B 992 GLN

Total number of N/Q/H flips: 25

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.046393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.030981 restraints weight = 386095.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.033351 restraints weight = 168104.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.035081 restraints weight = 101849.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.036351 restraints weight = 71275.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.037317 restraints weight = 54251.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2971
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2971 r_free = 0.2971    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (12 function evaluations)
r_final: 0.2946
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.3269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  17044  Z= 0.178
  Angle     :  0.764  24.053  23153  Z= 0.378
  Chirality :  0.041   0.184   2484
  Planarity :  0.007   0.190   2995
  Dihedral  :  8.116  88.083   2305
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 38.79
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.85 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.11 %
    Favored  : 98.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.18), residues: 2086
  helix:  0.57 (0.16), residues: 967
  sheet: -0.24 (0.29), residues: 291
  loop : -0.90 (0.22), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 296 
 TYR   0.024   0.001   TYR A 613 
 PHE   0.013   0.002   PHE B  82 
 TRP   0.035   0.002   TRP B  96 
 HIS   0.006   0.001   HIS A 478 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00379 /  0.18 (17037)
  covalent geometry    : angle       0.76415 /  0.38 (23153)
  hydrogen bonds       : bond        0.04455 /  2.84 (  800)
  hydrogen bonds       : angle       5.81791 /  4.18 ( 2263)
  Misc. bond           : bond        0.01405 /  0.57 (    7)

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

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

  4172 Ramachandran restraints generated.
    2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4172 Ramachandran restraints generated.
    2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 164
  time to evaluate  : 0.490 
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
TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it.
   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  118 MET cc_start: 0.9477 (mpp) cc_final: 0.9123 (mpp)
REVERT: A  218 LYS cc_start: 0.9447 (mttt) cc_final: 0.9217 (mttt)
REVERT: A  261 PHE cc_start: 0.9017 (m-80) cc_final: 0.8247 (m-80)
REVERT: A  262 LEU cc_start: 0.9687 (mm) cc_final: 0.9479 (mm)
REVERT: A  353 LEU cc_start: 0.9226 (mt) cc_final: 0.9023 (tt)
REVERT: A  356 LEU cc_start: 0.8434 (mt) cc_final: 0.7805 (mp)
REVERT: A  357 ILE cc_start: 0.9062 (mt) cc_final: 0.8757 (mm)
REVERT: A  967 MET cc_start: 0.8179 (mmm) cc_final: 0.7918 (mmm)
REVERT: A 1005 MET cc_start: 0.9195 (mmp) cc_final: 0.8889 (mmm)
REVERT: A 1034 GLN cc_start: 0.9425 (tp-100) cc_final: 0.8896 (tp-100)
REVERT: B   20 LEU cc_start: 0.8841 (mt) cc_final: 0.8241 (tt)
REVERT: B   86 LEU cc_start: 0.9576 (mt) cc_final: 0.8766 (tp)
REVERT: B  118 MET cc_start: 0.9355 (mpp) cc_final: 0.8814 (mpp)
REVERT: B  185 MET cc_start: 0.9068 (ttt) cc_final: 0.8805 (ttt)
REVERT: B  237 MET cc_start: 0.9650 (mtm) cc_final: 0.9308 (mtp)
REVERT: B  417 MET cc_start: 0.9507 (mtm) cc_final: 0.8922 (mtp)
REVERT: B  960 LEU cc_start: 0.8688 (tp) cc_final: 0.8318 (mt)
REVERT: B  969 ASN cc_start: 0.8719 (t0) cc_final: 0.8516 (t0)
REVERT: B  992 GLN cc_start: 0.9300 (mt0) cc_final: 0.8967 (tp40)
REVERT: B 1034 GLN cc_start: 0.9005 (mt0) cc_final: 0.8796 (mm-40)
  outliers start: 4
  outliers final: 4
  residues processed: 167
  average time/residue: 0.1186
  time to fit residues: 31.2174
Evaluate side-chains
  129 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 125
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 41 optimal weight:    0.6980
   chunk 84 optimal weight:    7.9990
   chunk 180 optimal weight:   10.0000
   chunk 155 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 148 optimal weight:    0.0070
   chunk 153 optimal weight:    6.9990
   chunk 178 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 111 optimal weight:    8.9990
   overall best weight:    2.1402

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 109 GLN
A 992 GLN
A1021 HIS
B  27 GLN
B 519 HIS
B1021 HIS
B1034 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.041710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.027563 restraints weight = 435298.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.029690 restraints weight = 183242.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.031243 restraints weight = 109668.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.032396 restraints weight = 76402.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.033236 restraints weight = 58151.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2835
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2835 r_free = 0.2835    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       54 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.2834
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.4449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  17044  Z= 0.199
  Angle     :  0.771  26.806  23153  Z= 0.350
  Chirality :  0.039   0.180   2484
  Planarity :  0.006   0.174   2995
  Dihedral  :  6.946  85.423   2305
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 51.93
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.19 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.88 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.19), residues: 2086
  helix:  1.18 (0.17), residues: 968
  sheet:  0.06 (0.29), residues: 287
  loop : -0.72 (0.23), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 167 
 TYR   0.031   0.002   TYR B 305 
 PHE   0.018   0.002   PHE B 158 
 TRP   0.043   0.003   TRP A 550 
 HIS   0.021   0.002   HIS A 388 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00400 /  0.20 (17037)
  covalent geometry    : angle       0.77050 /  0.35 (23153)
  hydrogen bonds       : bond        0.03571 /  2.26 (  800)
  hydrogen bonds       : angle       5.29170 /  3.78 ( 2263)
  Misc. bond           : bond        0.03439 /  1.43 (    7)

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

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

  4172 Ramachandran restraints generated.
    2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4172 Ramachandran restraints generated.
    2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 134
  time to evaluate  : 0.764 
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
TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it.
   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  112 MET cc_start: 0.9676 (mmp) cc_final: 0.9302 (mtp)
REVERT: A  218 LYS cc_start: 0.9478 (mttt) cc_final: 0.9221 (mttt)
REVERT: A  261 PHE cc_start: 0.9002 (m-80) cc_final: 0.8241 (m-80)
REVERT: A  356 LEU cc_start: 0.8323 (mt) cc_final: 0.7773 (mp)
REVERT: A  357 ILE cc_start: 0.8805 (mt) cc_final: 0.8543 (mt)
REVERT: A  812 MET cc_start: 0.8336 (mmp) cc_final: 0.7932 (tpp)
REVERT: A  992 GLN cc_start: 0.9000 (mp10) cc_final: 0.8777 (mp10)
REVERT: A 1005 MET cc_start: 0.9052 (mmp) cc_final: 0.8772 (mmm)
REVERT: A 1034 GLN cc_start: 0.9228 (tp-100) cc_final: 0.9000 (tp-100)
REVERT: B   20 LEU cc_start: 0.9046 (mt) cc_final: 0.8396 (tt)
REVERT: B   30 MET cc_start: 0.8189 (mmm) cc_final: 0.6950 (tpt)
REVERT: B   86 LEU cc_start: 0.8797 (mt) cc_final: 0.8434 (tp)
REVERT: B  112 MET cc_start: 0.9134 (mmp) cc_final: 0.8918 (mmm)
REVERT: B  118 MET cc_start: 0.9438 (mpp) cc_final: 0.8954 (mpp)
REVERT: B  237 MET cc_start: 0.9654 (mtm) cc_final: 0.9196 (mtp)
REVERT: B  416 MET cc_start: 0.9732 (mmm) cc_final: 0.9293 (mmm)
REVERT: B  417 MET cc_start: 0.9543 (mtm) cc_final: 0.9053 (mtp)
REVERT: B  712 ASN cc_start: 0.9410 (m-40) cc_final: 0.9080 (p0)
REVERT: B  890 LEU cc_start: 0.9121 (mt) cc_final: 0.8737 (tp)
  outliers start: 2
  outliers final: 2
  residues processed: 136
  average time/residue: 0.1188
  time to fit residues: 24.8866
Evaluate side-chains
  101 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 114 optimal weight:    7.9990
   chunk 153 optimal weight:   10.0000
   chunk 11 optimal weight:    0.7980
   chunk 3 optimal weight:   10.0000
   chunk 175 optimal weight:    8.9990
   chunk 138 optimal weight:   10.0000
   chunk 63 optimal weight:    1.9990
   chunk 199 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 88 optimal weight:    3.9990
   chunk 119 optimal weight:    2.9990
   overall best weight:    2.7588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 310 GLN    A
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 665 ASN
** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 841 GLN
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 310 GLN    A ** both conformations clash, **PLEASE CHECK MANUALLY**
B 841 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.039962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.026602 restraints weight = 422813.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.028590 restraints weight = 181941.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.030037 restraints weight = 110447.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.031119 restraints weight = 77803.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.031924 restraints weight = 59535.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2793
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2793 r_free = 0.2793    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       54 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2793 r_free = 0.2793    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       54 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.2793
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.5295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.086  17044  Z= 0.221
  Angle     :  0.762  25.257  23153  Z= 0.347
  Chirality :  0.038   0.170   2484
  Planarity :  0.006   0.173   2995
  Dihedral  :  6.720  68.761   2305
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 62.38
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.00 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.18), residues: 2086
  helix:  1.00 (0.16), residues: 970
  sheet: -0.14 (0.31), residues: 256
  loop : -0.89 (0.22), residues: 860

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 471 
 TYR   0.032   0.002   TYR A 997 
 PHE   0.016   0.002   PHE A 934 
 TRP   0.024   0.002   TRP B  96 
 HIS   0.009   0.002   HIS A 961 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00446 /  0.22 (17037)
  covalent geometry    : angle       0.76200 /  0.35 (23153)
  hydrogen bonds       : bond        0.03551 /  2.29 (  800)
  hydrogen bonds       : angle       5.34156 /  3.81 ( 2263)
  Misc. bond           : bond        0.03774 /  1.55 (    7)

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

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

  4172 Ramachandran restraints generated.
    2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4172 Ramachandran restraints generated.
    2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.673 
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
TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.9402 (mpp) cc_final: 0.9069 (mpp)
REVERT: A  145 MET cc_start: 0.9438 (mmp) cc_final: 0.9236 (mmp)
REVERT: A  218 LYS cc_start: 0.9494 (mttt) cc_final: 0.9254 (mttt)
REVERT: A  261 PHE cc_start: 0.9106 (m-80) cc_final: 0.8617 (m-80)
REVERT: A  262 LEU cc_start: 0.9673 (mm) cc_final: 0.9473 (mm)
REVERT: A  356 LEU cc_start: 0.8073 (mt) cc_final: 0.7769 (mt)
REVERT: A  357 ILE cc_start: 0.9116 (mt) cc_final: 0.8909 (mt)
REVERT: A  416 MET cc_start: 0.9618 (mmp) cc_final: 0.9112 (mmm)
REVERT: A  505 MET cc_start: 0.9634 (tpp) cc_final: 0.9229 (mmm)
REVERT: A  900 MET cc_start: 0.8017 (mmp) cc_final: 0.7562 (mpp)
REVERT: A 1005 MET cc_start: 0.8990 (mmp) cc_final: 0.8789 (mmm)
REVERT: B   20 LEU cc_start: 0.8882 (mt) cc_final: 0.8231 (tp)
REVERT: B  118 MET cc_start: 0.9413 (mpp) cc_final: 0.8853 (mpp)
REVERT: B  185 MET cc_start: 0.8974 (ttm) cc_final: 0.8584 (ttp)
REVERT: B  212 MET cc_start: 0.9715 (mmp) cc_final: 0.9303 (mmm)
REVERT: B  237 MET cc_start: 0.9602 (mtm) cc_final: 0.9210 (mtp)
REVERT: B  261 PHE cc_start: 0.9565 (m-80) cc_final: 0.8682 (m-80)
REVERT: B  354 MET cc_start: 0.8649 (tpt) cc_final: 0.8359 (tpt)
REVERT: B  416 MET cc_start: 0.9580 (mmm) cc_final: 0.9118 (mmm)
REVERT: B  417 MET cc_start: 0.9389 (mtm) cc_final: 0.9165 (ptp)
REVERT: B  821 LEU cc_start: 0.8732 (mt) cc_final: 0.8497 (mt)
REVERT: B  890 LEU cc_start: 0.9125 (mt) cc_final: 0.8619 (tp)
REVERT: B 1034 GLN cc_start: 0.9003 (mt0) cc_final: 0.8774 (mm-40)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1073
  time to fit residues: 19.2780
Evaluate side-chains
  89 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 124 optimal weight:    7.9990
   chunk 55 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 176 optimal weight:    5.9990
   chunk 47 optimal weight:   10.0000
   chunk 136 optimal weight:   10.0000
   chunk 109 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 573 ASN
** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 GLN
** B 310 GLN    A ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.037547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2554 r_free = 0.2554 target = 0.025018 restraints weight = 444357.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2626 r_free = 0.2626 target = 0.026886 restraints weight = 190508.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.028213 restraints weight = 115108.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.029200 restraints weight = 81108.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.029926 restraints weight = 62196.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2723
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       54 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       54 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.2723
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.6405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.118  17044  Z= 0.295
  Angle     :  0.907  27.492  23153  Z= 0.418
  Chirality :  0.041   0.182   2484
  Planarity :  0.007   0.143   2995
  Dihedral  :  7.074  83.779   2305
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 82.83
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.23 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  1.06 %
    Favored  : 98.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.18), residues: 2086
  helix:  0.21 (0.16), residues: 967
  sheet: -0.44 (0.32), residues: 257
  loop : -1.20 (0.21), residues: 862

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B1029 
 TYR   0.031   0.003   TYR B 829 
 PHE   0.025   0.003   PHE B 107 
 TRP   0.029   0.003   TRP B  96 
 HIS   0.011   0.002   HIS B 977 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00589 /  0.29 (17037)
  covalent geometry    : angle       0.90692 /  0.42 (23153)
  hydrogen bonds       : bond        0.03939 /  2.51 (  800)
  hydrogen bonds       : angle       5.76676 /  4.12 ( 2263)
  Misc. bond           : bond        0.04570 /  1.92 (    7)

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

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

  4172 Ramachandran restraints generated.
    2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4172 Ramachandran restraints generated.
    2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.9431 (mpp) cc_final: 0.9116 (mpp)
REVERT: A  145 MET cc_start: 0.9589 (mmp) cc_final: 0.9352 (mmp)
REVERT: A  261 PHE cc_start: 0.9111 (m-80) cc_final: 0.8572 (m-80)
REVERT: A  356 LEU cc_start: 0.8095 (mt) cc_final: 0.7606 (mt)
REVERT: A  357 ILE cc_start: 0.8960 (mt) cc_final: 0.8666 (mp)
REVERT: A  416 MET cc_start: 0.9636 (mmp) cc_final: 0.9195 (mmm)
REVERT: A  996 PHE cc_start: 0.8833 (t80) cc_final: 0.8595 (t80)
REVERT: A 1034 GLN cc_start: 0.9537 (tp-100) cc_final: 0.9313 (tp-100)
REVERT: B   20 LEU cc_start: 0.9153 (mt) cc_final: 0.8463 (tp)
REVERT: B  112 MET cc_start: 0.9567 (mmp) cc_final: 0.9199 (mmm)
REVERT: B  118 MET cc_start: 0.9518 (mpp) cc_final: 0.8852 (mpp)
REVERT: B  185 MET cc_start: 0.9006 (ttm) cc_final: 0.8602 (ttp)
REVERT: B  237 MET cc_start: 0.9544 (mtm) cc_final: 0.9272 (mtp)
REVERT: B  416 MET cc_start: 0.9670 (mmm) cc_final: 0.9264 (mmm)
REVERT: B  811 GLU cc_start: 0.9572 (mt-10) cc_final: 0.9114 (mp0)
  outliers start: 1
  outliers final: 1
  residues processed: 100
  average time/residue: 0.1131
  time to fit residues: 18.0940
Evaluate side-chains
  78 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 204 optimal weight:    0.4980
   chunk 36 optimal weight:    9.9990
   chunk 156 optimal weight:    7.9990
   chunk 64 optimal weight:    0.7980
   chunk 99 optimal weight:    0.7980
   chunk 179 optimal weight:    0.0670
   chunk 183 optimal weight:   30.0000
   chunk 148 optimal weight:    9.9990
   chunk 108 optimal weight:    5.9990
   chunk 192 optimal weight:    0.5980
   overall best weight:    0.5518

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 206 GLN
** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1022 GLN
B  70 ASN
B 109 GLN
B 204 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.039192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2596 r_free = 0.2596 target = 0.025902 restraints weight = 444528.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.027927 restraints weight = 181146.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.029392 restraints weight = 107290.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.030492 restraints weight = 74509.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.031312 restraints weight = 56438.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2782
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2782 r_free = 0.2782    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       54 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2782 r_free = 0.2782    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       54 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2782
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.6261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.068  17044  Z= 0.096
  Angle     :  0.552  17.442  23153  Z= 0.265
  Chirality :  0.037   0.197   2484
  Planarity :  0.006   0.157   2995
  Dihedral  :  6.313  77.576   2305
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 58.94
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.27 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.19), residues: 2086
  helix:  1.34 (0.17), residues: 966
  sheet: -0.17 (0.33), residues: 255
  loop : -0.79 (0.22), residues: 865

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 296 
 TYR   0.018   0.001   TYR A 613 
 PHE   0.027   0.001   PHE B  82 
 TRP   0.016   0.001   TRP B  96 
 HIS   0.004   0.001   HIS B 961 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00219 /  0.10 (17037)
  covalent geometry    : angle       0.55186 /  0.26 (23153)
  hydrogen bonds       : bond        0.03130 /  1.98 (  800)
  hydrogen bonds       : angle       5.04314 /  3.59 ( 2263)
  Misc. bond           : bond        0.00871 /  0.37 (    7)

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

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

  4172 Ramachandran restraints generated.
    2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4172 Ramachandran restraints generated.
    2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 MET cc_start: 0.9719 (mtm) cc_final: 0.8981 (ptp)
REVERT: A  118 MET cc_start: 0.9453 (mpp) cc_final: 0.9192 (mpp)
REVERT: A  145 MET cc_start: 0.9508 (mmp) cc_final: 0.9234 (mmp)
REVERT: A  261 PHE cc_start: 0.9127 (m-80) cc_final: 0.8805 (m-80)
REVERT: A  356 LEU cc_start: 0.8052 (mt) cc_final: 0.7530 (mp)
REVERT: A  357 ILE cc_start: 0.9082 (mt) cc_final: 0.8788 (mp)
REVERT: A  416 MET cc_start: 0.9557 (mmp) cc_final: 0.9253 (mmm)
REVERT: A  417 MET cc_start: 0.9717 (mtm) cc_final: 0.9181 (mtp)
REVERT: A  547 PHE cc_start: 0.9632 (t80) cc_final: 0.8703 (t80)
REVERT: A  781 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8635 (pp20)
REVERT: A  900 MET cc_start: 0.8714 (mmp) cc_final: 0.8409 (mmp)
REVERT: A  951 ASN cc_start: 0.9471 (m110) cc_final: 0.9235 (p0)
REVERT: A  979 MET cc_start: 0.9429 (mmp) cc_final: 0.9106 (mmm)
REVERT: A  996 PHE cc_start: 0.8771 (t80) cc_final: 0.8563 (t80)
REVERT: B   20 LEU cc_start: 0.9090 (mt) cc_final: 0.8435 (tp)
REVERT: B  112 MET cc_start: 0.9522 (mmp) cc_final: 0.9108 (mmm)
REVERT: B  118 MET cc_start: 0.9472 (mpp) cc_final: 0.8689 (mpp)
REVERT: B  185 MET cc_start: 0.8968 (ttm) cc_final: 0.8569 (ttp)
REVERT: B  409 GLU cc_start: 0.9208 (pp20) cc_final: 0.8888 (pp20)
REVERT: B  416 MET cc_start: 0.9604 (mmm) cc_final: 0.9094 (mmm)
REVERT: B  712 ASN cc_start: 0.9033 (m-40) cc_final: 0.8476 (p0)
REVERT: B  811 GLU cc_start: 0.9339 (mt-10) cc_final: 0.9023 (mp0)
REVERT: B  821 LEU cc_start: 0.9116 (mt) cc_final: 0.8834 (mt)
REVERT: B  960 LEU cc_start: 0.8628 (tp) cc_final: 0.8352 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1141
  time to fit residues: 18.6884
Evaluate side-chains
  87 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 110 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 175 optimal weight:   10.0000
   chunk 97 optimal weight:    1.9990
   chunk 131 optimal weight:    4.9990
   chunk 121 optimal weight:    1.9990
   chunk 116 optimal weight:    5.9990
   chunk 119 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0000
   chunk 10 optimal weight:    4.9990
   overall best weight:    0.6986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.039128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2595 r_free = 0.2595 target = 0.025875 restraints weight = 452657.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.027899 restraints weight = 182432.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.029403 restraints weight = 107539.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.030487 restraints weight = 74072.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.031317 restraints weight = 56266.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2783
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       54 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (10 function evaluations)
r_final: 0.2783
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.6350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.058  17044  Z= 0.094
  Angle     :  0.508  11.699  23153  Z= 0.247
  Chirality :  0.036   0.135   2484
  Planarity :  0.004   0.048   2995
  Dihedral  :  6.036  73.631   2305
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 57.60
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.19 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.85 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.19), residues: 2086
  helix:  1.86 (0.17), residues: 966
  sheet: -0.16 (0.33), residues: 255
  loop : -0.64 (0.23), residues: 865

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 471 
 TYR   0.014   0.001   TYR A 613 
 PHE   0.009   0.001   PHE B 331 
 TRP   0.015   0.001   TRP B  96 
 HIS   0.004   0.001   HIS B 961 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00212 /  0.09 (17037)
  covalent geometry    : angle       0.50820 /  0.25 (23153)
  hydrogen bonds       : bond        0.02823 /  1.81 (  800)
  hydrogen bonds       : angle       4.81669 /  3.45 ( 2263)
  Misc. bond           : bond        0.01284 /  0.52 (    7)

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

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

  4172 Ramachandran restraints generated.
    2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4172 Ramachandran restraints generated.
    2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 MET cc_start: 0.7151 (ptm) cc_final: 0.6857 (ptm)
REVERT: A  112 MET cc_start: 0.9669 (mtm) cc_final: 0.8934 (ptp)
REVERT: A  118 MET cc_start: 0.9427 (mpp) cc_final: 0.8937 (mtm)
REVERT: A  145 MET cc_start: 0.9481 (mmp) cc_final: 0.9240 (mmp)
REVERT: A  261 PHE cc_start: 0.9138 (m-80) cc_final: 0.8814 (m-80)
REVERT: A  356 LEU cc_start: 0.8297 (mt) cc_final: 0.8040 (mt)
REVERT: A  357 ILE cc_start: 0.8916 (mt) cc_final: 0.8639 (mp)
REVERT: A  416 MET cc_start: 0.9573 (mmp) cc_final: 0.9279 (mmm)
REVERT: A  417 MET cc_start: 0.9699 (mtm) cc_final: 0.9057 (ptp)
REVERT: A  767 MET cc_start: 0.8747 (ptp) cc_final: 0.8455 (ptp)
REVERT: A  781 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8584 (mp0)
REVERT: A  900 MET cc_start: 0.8872 (mmp) cc_final: 0.8585 (mmp)
REVERT: A  951 ASN cc_start: 0.9462 (m110) cc_final: 0.9212 (p0)
REVERT: A  979 MET cc_start: 0.9398 (mmp) cc_final: 0.8917 (mmm)
REVERT: B   20 LEU cc_start: 0.9091 (mt) cc_final: 0.8448 (tp)
REVERT: B  112 MET cc_start: 0.9503 (mmp) cc_final: 0.9110 (mmm)
REVERT: B  118 MET cc_start: 0.9440 (mpp) cc_final: 0.8606 (mpp)
REVERT: B  185 MET cc_start: 0.8927 (ttm) cc_final: 0.8509 (ttp)
REVERT: B  237 MET cc_start: 0.9606 (mtm) cc_final: 0.9350 (mtp)
REVERT: B  416 MET cc_start: 0.9646 (mmm) cc_final: 0.9178 (mmm)
REVERT: B  712 ASN cc_start: 0.9032 (m-40) cc_final: 0.8477 (p0)
REVERT: B  811 GLU cc_start: 0.9345 (mt-10) cc_final: 0.9007 (mp0)
REVERT: B  960 LEU cc_start: 0.8667 (tp) cc_final: 0.8361 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1244
  time to fit residues: 20.7281
Evaluate side-chains
  87 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 184 optimal weight:    5.9990
   chunk 185 optimal weight:    3.9990
   chunk 186 optimal weight:    5.9990
   chunk 172 optimal weight:    0.7980
   chunk 41 optimal weight:    6.9990
   chunk 77 optimal weight:    5.9990
   chunk 141 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 123 optimal weight:    5.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 872 GLN
** B 310 GLN    A ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.037929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2561 r_free = 0.2561 target = 0.025116 restraints weight = 476534.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2637 r_free = 0.2637 target = 0.027068 restraints weight = 191025.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.028491 restraints weight = 112581.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.029543 restraints weight = 77848.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2753 r_free = 0.2753 target = 0.030284 restraints weight = 59123.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2740
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2740 r_free = 0.2740    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2740 r_free = 0.2740    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.2740
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.6785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085  17044  Z= 0.177
  Angle     :  0.660  22.833  23153  Z= 0.298
  Chirality :  0.037   0.168   2484
  Planarity :  0.004   0.051   2995
  Dihedral  :  6.151  79.143   2305
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 70.72
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.35 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.85 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.19), residues: 2086
  helix:  1.51 (0.17), residues: 971
  sheet: -0.34 (0.33), residues: 257
  loop : -0.73 (0.23), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 296 
 TYR   0.025   0.002   TYR B 829 
 PHE   0.014   0.002   PHE B 107 
 TRP   0.018   0.002   TRP B  96 
 HIS   0.008   0.001   HIS B 961 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.18 (17037)
  covalent geometry    : angle       0.65967 /  0.30 (23153)
  hydrogen bonds       : bond        0.03000 /  1.90 (  800)
  hydrogen bonds       : angle       4.98543 /  3.57 ( 2263)
  Misc. bond           : bond        0.03118 /  1.31 (    7)

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

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

  4172 Ramachandran restraints generated.
    2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4172 Ramachandran restraints generated.
    2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 MET cc_start: 0.6951 (ptm) cc_final: 0.6160 (ttp)
REVERT: A  112 MET cc_start: 0.9606 (mtm) cc_final: 0.8983 (mtp)
REVERT: A  118 MET cc_start: 0.9388 (mpp) cc_final: 0.8895 (mtm)
REVERT: A  145 MET cc_start: 0.9538 (mmp) cc_final: 0.9245 (mmp)
REVERT: A  261 PHE cc_start: 0.9108 (m-80) cc_final: 0.8822 (m-80)
REVERT: A  356 LEU cc_start: 0.7901 (mt) cc_final: 0.7448 (mt)
REVERT: A  357 ILE cc_start: 0.8868 (mt) cc_final: 0.8616 (mp)
REVERT: A  416 MET cc_start: 0.9613 (mmp) cc_final: 0.9313 (mmm)
REVERT: A  417 MET cc_start: 0.9712 (mtm) cc_final: 0.9184 (mtp)
REVERT: A  781 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8752 (mt-10)
REVERT: A  900 MET cc_start: 0.8984 (mmp) cc_final: 0.8757 (mmp)
REVERT: A  979 MET cc_start: 0.9339 (mmp) cc_final: 0.9038 (mmm)
REVERT: A  996 PHE cc_start: 0.8532 (t80) cc_final: 0.8300 (t80)
REVERT: B  112 MET cc_start: 0.9487 (mmp) cc_final: 0.9115 (mmm)
REVERT: B  118 MET cc_start: 0.9445 (mpp) cc_final: 0.8656 (mpp)
REVERT: B  185 MET cc_start: 0.8928 (ttm) cc_final: 0.8427 (ttp)
REVERT: B  237 MET cc_start: 0.9550 (mtm) cc_final: 0.9291 (mtp)
REVERT: B  416 MET cc_start: 0.9634 (mmm) cc_final: 0.9197 (mmm)
REVERT: B  712 ASN cc_start: 0.9151 (m-40) cc_final: 0.8560 (p0)
REVERT: B  811 GLU cc_start: 0.9432 (mt-10) cc_final: 0.9225 (pm20)
REVERT: B  960 LEU cc_start: 0.8677 (tp) cc_final: 0.8367 (mt)
REVERT: B 1034 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8634 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.1211
  time to fit residues: 18.5814
Evaluate side-chains
  75 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 137 optimal weight:    0.0170
   chunk 106 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 192 optimal weight:    0.9990
   chunk 123 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 172 optimal weight:    0.8980
   chunk 98 optimal weight:    7.9990
   overall best weight:    0.7620

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 310 GLN    A

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.038627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2584 r_free = 0.2584 target = 0.025606 restraints weight = 445403.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.027579 restraints weight = 181964.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.029042 restraints weight = 108008.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.030132 restraints weight = 74768.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.030900 restraints weight = 56570.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2769
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2769 r_free = 0.2769    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2769 r_free = 0.2769    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.2769
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.6757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.069  17044  Z= 0.090
  Angle     :  0.488  12.013  23153  Z= 0.240
  Chirality :  0.036   0.153   2484
  Planarity :  0.004   0.048   2995
  Dihedral  :  5.925  76.843   2305
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 59.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.85 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.19), residues: 2086
  helix:  1.97 (0.17), residues: 964
  sheet: -0.25 (0.34), residues: 255
  loop : -0.65 (0.22), residues: 867

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 471 
 TYR   0.015   0.001   TYR A 613 
 PHE   0.013   0.001   PHE B  82 
 TRP   0.011   0.001   TRP B  96 
 HIS   0.004   0.001   HIS B 961 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00211 /  0.09 (17037)
  covalent geometry    : angle       0.48835 /  0.24 (23153)
  hydrogen bonds       : bond        0.02740 /  1.73 (  800)
  hydrogen bonds       : angle       4.73908 /  3.39 ( 2263)
  Misc. bond           : bond        0.01137 /  0.47 (    7)

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

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

  4172 Ramachandran restraints generated.
    2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4172 Ramachandran restraints generated.
    2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 MET cc_start: 0.6784 (ptm) cc_final: 0.5994 (ttp)
REVERT: A  112 MET cc_start: 0.9609 (mtm) cc_final: 0.9256 (mmp)
REVERT: A  118 MET cc_start: 0.9447 (mpp) cc_final: 0.8981 (mtm)
REVERT: A  145 MET cc_start: 0.9498 (mmp) cc_final: 0.9255 (mmp)
REVERT: A  261 PHE cc_start: 0.9094 (m-80) cc_final: 0.8821 (m-80)
REVERT: A  316 MET cc_start: 0.8984 (mmt) cc_final: 0.8650 (ttm)
REVERT: A  356 LEU cc_start: 0.7964 (mt) cc_final: 0.7460 (mt)
REVERT: A  357 ILE cc_start: 0.8915 (mt) cc_final: 0.8621 (mp)
REVERT: A  416 MET cc_start: 0.9593 (mmp) cc_final: 0.9288 (mmm)
REVERT: A  417 MET cc_start: 0.9731 (mtm) cc_final: 0.9085 (ptp)
REVERT: A  547 PHE cc_start: 0.9604 (t80) cc_final: 0.9144 (t80)
REVERT: A  767 MET cc_start: 0.8686 (ptp) cc_final: 0.8407 (ptp)
REVERT: A  781 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8685 (mp0)
REVERT: A  900 MET cc_start: 0.8916 (mmp) cc_final: 0.8660 (mmp)
REVERT: A  951 ASN cc_start: 0.9451 (m110) cc_final: 0.9225 (p0)
REVERT: A  967 MET cc_start: 0.7046 (mmm) cc_final: 0.5913 (mmm)
REVERT: A  979 MET cc_start: 0.9337 (mmp) cc_final: 0.8907 (mmm)
REVERT: B  112 MET cc_start: 0.9464 (mmp) cc_final: 0.9096 (mmm)
REVERT: B  118 MET cc_start: 0.9491 (mpp) cc_final: 0.8668 (mpp)
REVERT: B  185 MET cc_start: 0.8896 (ttm) cc_final: 0.8395 (ttp)
REVERT: B  237 MET cc_start: 0.9648 (mtm) cc_final: 0.9323 (mtp)
REVERT: B  409 GLU cc_start: 0.9168 (pp20) cc_final: 0.8817 (pp20)
REVERT: B  416 MET cc_start: 0.9625 (mmm) cc_final: 0.9112 (mmm)
REVERT: B  712 ASN cc_start: 0.9049 (m-40) cc_final: 0.8797 (p0)
REVERT: B  811 GLU cc_start: 0.9378 (mt-10) cc_final: 0.9030 (mp0)
REVERT: B  960 LEU cc_start: 0.8560 (tp) cc_final: 0.8328 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1150
  time to fit residues: 20.1252
Evaluate side-chains
  84 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 148 optimal weight:    0.9980
   chunk 43 optimal weight:    7.9990
   chunk 23 optimal weight:    0.0970
   chunk 95 optimal weight:   20.0000
   chunk 126 optimal weight:    0.0070
   chunk 66 optimal weight:    9.9990
   chunk 123 optimal weight:    0.9980
   chunk 9 optimal weight:    6.9990
   chunk 96 optimal weight:    0.9990
   chunk 202 optimal weight:    3.9990
   chunk 103 optimal weight:   10.0000
   overall best weight:    0.6198

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.038826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2593 r_free = 0.2593 target = 0.025827 restraints weight = 413735.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.027774 restraints weight = 176120.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2720 r_free = 0.2720 target = 0.029204 restraints weight = 105954.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.030265 restraints weight = 74032.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.031073 restraints weight = 56639.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2772
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2772 r_free = 0.2772    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2772 r_free = 0.2772    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2772
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.6796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.059  17044  Z= 0.084
  Angle     :  0.477  11.024  23153  Z= 0.236
  Chirality :  0.036   0.157   2484
  Planarity :  0.004   0.047   2995
  Dihedral  :  5.689  73.366   2305
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 58.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.85 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.20), residues: 2086
  helix:  2.18 (0.17), residues: 965
  sheet: -0.23 (0.34), residues: 255
  loop : -0.58 (0.23), residues: 866

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 471 
 TYR   0.013   0.001   TYR A 613 
 PHE   0.016   0.001   PHE A 405 
 TRP   0.011   0.001   TRP B  96 
 HIS   0.003   0.000   HIS B 961 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00199 /  0.08 (17037)
  covalent geometry    : angle       0.47721 /  0.24 (23153)
  hydrogen bonds       : bond        0.02618 /  1.65 (  800)
  hydrogen bonds       : angle       4.63244 /  3.31 ( 2263)
  Misc. bond           : bond        0.01109 /  0.46 (    7)

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

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

  4172 Ramachandran restraints generated.
    2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4172 Ramachandran restraints generated.
    2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 MET cc_start: 0.6597 (ptm) cc_final: 0.5922 (ttp)
REVERT: A  112 MET cc_start: 0.9725 (mtm) cc_final: 0.9367 (mmp)
REVERT: A  118 MET cc_start: 0.9438 (mpp) cc_final: 0.8939 (mtm)
REVERT: A  145 MET cc_start: 0.9484 (mmp) cc_final: 0.9248 (mmp)
REVERT: A  261 PHE cc_start: 0.9163 (m-80) cc_final: 0.8898 (m-80)
REVERT: A  356 LEU cc_start: 0.8020 (mt) cc_final: 0.7676 (mt)
REVERT: A  416 MET cc_start: 0.9599 (mmp) cc_final: 0.9274 (mmp)
REVERT: A  417 MET cc_start: 0.9734 (mtm) cc_final: 0.9102 (ptp)
REVERT: A  781 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8761 (pp20)
REVERT: A  900 MET cc_start: 0.8869 (mmp) cc_final: 0.8643 (mmp)
REVERT: A  951 ASN cc_start: 0.9446 (m110) cc_final: 0.9226 (p0)
REVERT: A  967 MET cc_start: 0.7056 (mmm) cc_final: 0.5936 (mmm)
REVERT: A  979 MET cc_start: 0.9310 (mmp) cc_final: 0.8883 (mmm)
REVERT: B  112 MET cc_start: 0.9496 (mmp) cc_final: 0.9125 (mmm)
REVERT: B  118 MET cc_start: 0.9470 (mpp) cc_final: 0.8639 (mpp)
REVERT: B  185 MET cc_start: 0.8843 (ttm) cc_final: 0.8347 (ttp)
REVERT: B  409 GLU cc_start: 0.9184 (pp20) cc_final: 0.8830 (pp20)
REVERT: B  416 MET cc_start: 0.9658 (mmm) cc_final: 0.9192 (mmm)
REVERT: B  712 ASN cc_start: 0.9207 (m-40) cc_final: 0.8985 (p0)
REVERT: B  811 GLU cc_start: 0.9359 (mt-10) cc_final: 0.9016 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1175
  time to fit residues: 19.6219
Evaluate side-chains
  84 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 2 optimal weight:    0.2980
   chunk 34 optimal weight:    1.9990
   chunk 192 optimal weight:    6.9990
   chunk 181 optimal weight:    7.9990
   chunk 111 optimal weight:    5.9990
   chunk 167 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0270
   chunk 37 optimal weight:    0.0870
   chunk 92 optimal weight:    9.9990
   overall best weight:    1.2820

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 724 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.038394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2569 r_free = 0.2569 target = 0.025192 restraints weight = 535214.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.027229 restraints weight = 199145.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.028727 restraints weight = 114775.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.029832 restraints weight = 78312.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.030648 restraints weight = 58820.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2759
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.2759
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.6948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  17044  Z= 0.112
  Angle     :  0.512  14.750  23153  Z= 0.244
  Chirality :  0.036   0.152   2484
  Planarity :  0.004   0.047   2995
  Dihedral  :  5.652  73.928   2305
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 62.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.93 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.20), residues: 2086
  helix:  2.16 (0.17), residues: 965
  sheet: -0.22 (0.34), residues: 255
  loop : -0.59 (0.23), residues: 866

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 296 
 TYR   0.013   0.001   TYR A 613 
 PHE   0.015   0.001   PHE A 405 
 TRP   0.012   0.001   TRP B  96 
 HIS   0.008   0.001   HIS A 408 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.11 (17037)
  covalent geometry    : angle       0.51230 /  0.24 (23153)
  hydrogen bonds       : bond        0.02649 /  1.67 (  800)
  hydrogen bonds       : angle       4.64834 /  3.32 ( 2263)
  Misc. bond           : bond        0.01893 /  0.77 (    7)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2578.32 seconds
wall clock time: 46 minutes 1.86 seconds (2761.86 seconds total)