Starting phenix.real_space_refine
on Thu May 15 15:43:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j86_36061/05_2025/8j86_36061.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j86_36061/05_2025/8j86_36061.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j86_36061/05_2025/8j86_36061.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j86_36061/05_2025/8j86_36061.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j86_36061/05_2025/8j86_36061.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j86_36061/05_2025/8j86_36061.cif"
  }
  resolution = 3.22
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      3      9.91       5
     P      35      5.49       5
     S      67      5.16       5
     C    8456      2.51       5
     N    2225      2.21       5
     O    2581      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13367
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 8132
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 993, 8132
          Classifications: {'peptide': 993}
          Link IDs: {'PTRANS': 36, 'TRANS': 956}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 1686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1686
          Classifications: {'peptide': 209}
          Incomplete info: {'backbone_only': 2}
          Link IDs: {'PTRANS': 13, 'TRANS': 195}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "C"
      Number of atoms: 2830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 2830
          Classifications: {'peptide': 350}
          Link IDs: {'PTRANS': 8, 'TRANS': 341}
          Chain breaks: 10
    Chain: "P"
      Number of atoms: 291
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 291
          Classifications: {'DNA': 14}
          Link IDs: {'rna3p': 13}
    Chain: "T"
      Number of atoms: 425
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 425
          Classifications: {'DNA': 21}
          Link IDs: {'rna3p': 20}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Residues with excluded nonbonded symmetry interactions: 13
    residue:
      pdb=" P    DT P  17 " occ=0.04
      ... (18 atoms not shown)
      pdb=" C6   DT P  17 " occ=0.04
    residue:
      pdb=" P    DT P  18 " occ=0.19
      ... (18 atoms not shown)
      pdb=" C6   DT P  18 " occ=0.19
    residue:
      pdb=" P    DA P  19 " occ=0.49
      ... (19 atoms not shown)
      pdb=" C4   DA P  19 " occ=0.49
    residue:
      pdb=" P    DA P  20 " occ=0.68
      ... (19 atoms not shown)
      pdb=" C4   DA P  20 " occ=0.68
    residue:
      pdb=" P    DT T   1 " occ=0.32
      ... (18 atoms not shown)
      pdb=" C6   DT T   1 " occ=0.32
    residue:
      pdb=" P    DT T   2 " occ=0.67
      ... (18 atoms not shown)
      pdb=" C6   DT T   2 " occ=0.67
    residue:
      pdb=" P    DG T   3 " occ=0.68
      ... (20 atoms not shown)
      pdb=" C4   DG T   3 " occ=0.68
    residue:
      pdb=" P    DA T   4 " occ=0.72
      ... (19 atoms not shown)
      pdb=" C4   DA T   4 " occ=0.72
    residue:
      pdb=" P    DT T   5 " occ=0.49
      ... (18 atoms not shown)
      pdb=" C6   DT T   5 " occ=0.49
    residue:
      pdb=" P    DC T  14 " occ=0.81
      ... (17 atoms not shown)
      pdb=" C6   DC T  14 " occ=0.81
    residue:
      pdb=" P    DT T  15 " occ=0.33
      ... (18 atoms not shown)
      pdb=" C6   DT T  15 " occ=0.33
    residue:
      pdb=" P    DC T  16 " occ=0.89
      ... (17 atoms not shown)
      pdb=" C6   DC T  16 " occ=0.89
    residue:
      pdb=" P    DA T  17 " occ=0.92
      ... (19 atoms not shown)
      pdb=" C4   DA T  17 " occ=0.92
  Time building chain proxies: 7.94, per 1000 atoms: 0.59
  Number of scatterers: 13367
  At special positions: 0
  Unit cell: (89.88, 113.4, 143.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      3     19.99
     S      67     16.00
     P      35     15.00
     O    2581      8.00
     N    2225      7.00
     C    8456      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.11
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2968

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 13 sheets defined
      36.1% alpha, 10.8% beta
      0 base pairs and 14 stacking pairs defined.
    Time for finding SS restraints: 4.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 48
      removed outlier: 3.773A  pdb=" N   TYR A  47 " --> pdb=" O   THR A  43 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLN A  48 " --> pdb=" O   ASP A  44 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 43 through 48'
    Processing helix  chain 'A' and resid 109 through 118
      removed outlier: 3.540A  pdb=" N   PHE A 113 " --> pdb=" O   ASN A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 220
    Processing helix  chain 'A' and resid 240 through 254
    Processing helix  chain 'A' and resid 267 through 280
    Processing helix  chain 'A' and resid 331 through 336
    Processing helix  chain 'A' and resid 345 through 354
    Processing helix  chain 'A' and resid 380 through 390
    Processing helix  chain 'A' and resid 439 through 446
    Processing helix  chain 'A' and resid 448 through 474
    Processing helix  chain 'A' and resid 474 through 487
    Processing helix  chain 'A' and resid 497 through 502
      removed outlier: 3.738A  pdb=" N   ILE A 502 " --> pdb=" O   ALA A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 514
    Processing helix  chain 'A' and resid 552 through 562
    Processing helix  chain 'A' and resid 564 through 566
      No H-bonds generated for 'chain 'A' and resid 564 through 566'
    Processing helix  chain 'A' and resid 579 through 591
    Processing helix  chain 'A' and resid 592 through 594
      No H-bonds generated for 'chain 'A' and resid 592 through 594'
    Processing helix  chain 'A' and resid 621 through 639
      removed outlier: 3.579A  pdb=" N   ARG A 628 " --> pdb=" O   PRO A 624 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LYS A 639 " --> pdb=" O   ALA A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 652
    Processing helix  chain 'A' and resid 655 through 665
    Processing helix  chain 'A' and resid 666 through 671
    Processing helix  chain 'A' and resid 680 through 700
    Processing helix  chain 'A' and resid 763 through 782
      removed outlier: 3.610A  pdb=" N   SER A 767 " --> pdb=" O   ASP A 763 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASN A 779 " --> pdb=" O   GLU A 775 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   SER A 780 " --> pdb=" O   ARG A 776 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 839 through 856
      removed outlier: 3.558A  pdb=" N   ILE A 843 " --> pdb=" O   HIS A 839 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLU A 852 " --> pdb=" O   THR A 848 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   GLU A 856 " --> pdb=" O   GLU A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 876
      removed outlier: 4.167A  pdb=" N   ILE A 866 " --> pdb=" O   ASN A 862 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   THR A 874 " --> pdb=" O   ARG A 870 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ASP A 875 " --> pdb=" O   SER A 871 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 877 through 881
      removed outlier: 3.501A  pdb=" N   PHE A 880 " --> pdb=" O   ARG A 877 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ASP A 881 " --> pdb=" O   SER A 878 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 877 through 881'
    Processing helix  chain 'A' and resid 886 through 890
    Processing helix  chain 'A' and resid 969 through 983
      removed outlier: 4.750A  pdb=" N   LYS A 973 " --> pdb=" O   GLU A 969 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 989 through 993
    Processing helix  chain 'B' and resid 19 through 38
      removed outlier: 3.932A  pdb=" N   MET B  23 " --> pdb=" O   TRP B  19 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   SER B  24 " --> pdb=" O   GLU B  20 " (cutoff:3.500A)
      removed outlier: 5.550A  pdb=" N   GLN B  25 " --> pdb=" O   PRO B  21 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLU B  28 " --> pdb=" O   SER B  24 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLU B  32 " --> pdb=" O   GLU B  28 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   VAL B  33 " --> pdb=" O   PHE B  29 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   SER B  35 " --> pdb=" O   ASN B  31 " (cutoff:3.500A)
      removed outlier: 5.436A  pdb=" N   TRP B  36 " --> pdb=" O   GLU B  32 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU B  38 " --> pdb=" O   ALA B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 54
      removed outlier: 3.507A  pdb=" N   LEU B  53 " --> pdb=" O   PHE B  50 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LYS B  54 " --> pdb=" O   ILE B  51 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 50 through 54'
    Processing helix  chain 'B' and resid 86 through 100
    Processing helix  chain 'B' and resid 137 through 151
      removed outlier: 3.757A  pdb=" N   LYS B 142 " --> pdb=" O   ASP B 138 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   LEU B 143 " --> pdb=" O   LYS B 139 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   HIS B 147 " --> pdb=" O   LEU B 143 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ILE B 148 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   HIS B 151 " --> pdb=" O   HIS B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 164
    Processing helix  chain 'B' and resid 195 through 205
      removed outlier: 3.666A  pdb=" N   ASN B 199 " --> pdb=" O   PHE B 195 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   GLU B 203 " --> pdb=" O   ASN B 199 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3 through 19
      removed outlier: 3.656A  pdb=" N   LYS C  18 " --> pdb=" O   LEU C  14 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   SER C  19 " --> pdb=" O   SER C  15 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 42
      removed outlier: 3.916A  pdb=" N   SER C  33 " --> pdb=" O   GLU C  29 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   SER C  40 " --> pdb=" O   GLU C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 106 through 108
      No H-bonds generated for 'chain 'C' and resid 106 through 108'
    Processing helix  chain 'C' and resid 109 through 114
    Processing helix  chain 'C' and resid 116 through 121
    Processing helix  chain 'C' and resid 147 through 158
      removed outlier: 4.038A  pdb=" N   ILE C 151 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 249 through 256
    Processing helix  chain 'C' and resid 288 through 297
    Processing helix  chain 'C' and resid 315 through 324
      removed outlier: 3.963A  pdb=" N   LEU C 319 " --> pdb=" O   GLY C 315 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 341
      removed outlier: 3.537A  pdb=" N   SER C 341 " --> pdb=" O   GLU C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 341 through 349
    Processing helix  chain 'C' and resid 352 through 362
    Processing helix  chain 'C' and resid 364 through 374
    Processing helix  chain 'C' and resid 392 through 396
    Processing helix  chain 'C' and resid 397 through 406
    Processing helix  chain 'C' and resid 406 through 424
      removed outlier: 3.592A  pdb=" N   PHE C 410 " --> pdb=" O   ASN C 406 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134
      removed outlier: 7.949A  pdb=" N   TYR A 140 " --> pdb=" O   THR A  29 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   PHE A  31 " --> pdb=" O   TYR A 140 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   PHE A  17 " --> pdb=" O   GLU A  10 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   GLU A  10 " --> pdb=" O   PHE A  17 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   TYR A  19 " --> pdb=" O   TRP A   8 " (cutoff:3.500A)
      removed outlier: 5.688A  pdb=" N   TRP A   8 " --> pdb=" O   TYR A  19 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   LYS A  21 " --> pdb=" O   ILE A   6 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   MET A   1 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   GLY A 123 " --> pdb=" O   CYS A   5 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   CYS A 124 " --> pdb=" O   ILE A 153 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ILE A 153 " --> pdb=" O   CYS A 124 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40
      removed outlier: 3.573A  pdb=" N   LEU A  90 " --> pdb=" O   ARG A  58 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   ASN A  56 " --> pdb=" O   GLU A  92 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66
    Processing sheet with id=AA4, first strand: chain 'A' and resid 72 through 73
      removed outlier: 3.630A  pdb=" N   SER A  73 " --> pdb=" O   VAL A 571 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL A 573 " --> pdb=" O   SER A  73 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ILE A 614 " --> pdb=" O   VAL A 569 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   VAL A 571 " --> pdb=" O   ILE A 612 " (cutoff:3.500A)
      removed outlier: 5.834A  pdb=" N   ILE A 612 " --> pdb=" O   VAL A 571 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   VAL A 573 " --> pdb=" O   SER A 610 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   SER A 610 " --> pdb=" O   VAL A 573 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 197 through 203
      removed outlier: 3.616A  pdb=" N   THR A 186 " --> pdb=" O   LEU A 202 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   PHE A 164 " --> pdb=" O   CYS A 189 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   VAL A 259 " --> pdb=" O   PHE A 329 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 303
    Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 359
    Processing sheet with id=AA8, first strand: chain 'A' and resid 705 through 706
      removed outlier: 6.092A  pdb=" N   SER A 747 " --> pdb=" O   GLU A 758 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   GLU A 758 " --> pdb=" O   SER A 747 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   TYR A 749 " --> pdb=" O   PHE A 756 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   ALA A 793 " --> pdb=" O   ILE A 547 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ASP A 549 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   PHE A 791 " --> pdb=" O   ASP A 549 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LYS A 796 " --> pdb=" O   MET A 809 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   LEU A 798 " --> pdb=" O   THR A 807 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   THR A 807 " --> pdb=" O   LEU A 798 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 120
      removed outlier: 6.267A  pdb=" N   VAL B  62 " --> pdb=" O   ILE B 117 " (cutoff:3.500A)
      removed outlier: 7.365A  pdb=" N   TRP B 119 " --> pdb=" O   VAL B  62 " (cutoff:3.500A)
      removed outlier: 5.717A  pdb=" N   VAL B  64 " --> pdb=" O   TRP B 119 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU B 158 " --> pdb=" O   CYS B  65 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   LEU B 155 " --> pdb=" O   ILE B 177 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   GLY B 179 " --> pdb=" O   LEU B 155 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   CYS B 157 " --> pdb=" O   GLY B 179 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 85 through 89
    Processing sheet with id=AB2, first strand: chain 'C' and resid 220 through 223
      removed outlier: 7.245A  pdb=" N   ILE C 238 " --> pdb=" O   GLU C 221 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LYS C 243 " --> pdb=" O   THR C 239 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 267 through 268
    Processing sheet with id=AB4, first strand: chain 'C' and resid 301 through 303

    411 hydrogen bonds defined for protein.
    1173 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      14 stacking parallelities
  Total time for adding SS restraints: 4.18

  Time building geometry restraints manager: 3.68 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3889
        1.34 -     1.45: 2293
        1.45 -     1.57: 7355
        1.57 -     1.69: 68
        1.69 -     1.81: 102
  Bond restraints: 13707
  Sorted by residual:
  bond pdb=" C3'  DA P  14 "
       pdb=" O3'  DA P  14 "
    ideal  model  delta    sigma   weight residual
    1.422  1.472 -0.050 3.00e-02 1.11e+03 2.74e+00
  bond pdb=" N   TYR C  60 "
       pdb=" CA  TYR C  60 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.016 1.29e-02 6.01e+03 1.62e+00
  bond pdb=" C   PRO A 593 "
       pdb=" N   PRO A 594 "
    ideal  model  delta    sigma   weight residual
    1.334  1.362 -0.028 2.34e-02 1.83e+03 1.43e+00
  bond pdb=" C3'  DA T  12 "
       pdb=" O3'  DA T  12 "
    ideal  model  delta    sigma   weight residual
    1.422  1.457 -0.035 3.00e-02 1.11e+03 1.34e+00
  bond pdb=" C3'  DC T  14 "
       pdb=" O3'  DC T  14 "
    ideal  model  delta    sigma   weight residual
    1.422  1.454 -0.032 3.00e-02 1.11e+03 1.14e+00
  ... (remaining 13702 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 18196
        1.44 -     2.87: 369
        2.87 -     4.31: 66
        4.31 -     5.75: 11
        5.75 -     7.19: 5
  Bond angle restraints: 18647
  Sorted by residual:
  angle pdb=" C   GLU A 339 "
        pdb=" CA  GLU A 339 "
        pdb=" CB  GLU A 339 "
      ideal   model   delta    sigma   weight residual
     116.34  110.36    5.98 1.40e+00 5.10e-01 1.83e+01
  angle pdb=" C   PRO C 107 "
        pdb=" N   ASP C 108 "
        pdb=" CA  ASP C 108 "
      ideal   model   delta    sigma   weight residual
     121.54  126.80   -5.26 1.91e+00 2.74e-01 7.58e+00
  angle pdb=" N   ASN B  83 "
        pdb=" CA  ASN B  83 "
        pdb=" C   ASN B  83 "
      ideal   model   delta    sigma   weight residual
     114.56  111.19    3.37 1.27e+00 6.20e-01 7.04e+00
  angle pdb=" C   TYR C  60 "
        pdb=" CA  TYR C  60 "
        pdb=" CB  TYR C  60 "
      ideal   model   delta    sigma   weight residual
     110.42  115.40   -4.98 1.99e+00 2.53e-01 6.26e+00
  angle pdb=" C3'  DA P  14 "
        pdb=" O3'  DA P  14 "
        pdb=" P    DG P  15 "
      ideal   model   delta    sigma   weight residual
     120.20  123.85   -3.65 1.50e+00 4.44e-01 5.91e+00
  ... (remaining 18642 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.64: 7930
       35.64 -    71.29: 256
       71.29 -   106.93: 14
      106.93 -   142.57: 2
      142.57 -   178.21: 2
  Dihedral angle restraints: 8204
    sinusoidal: 3616
      harmonic: 4588
  Sorted by residual:
  dihedral pdb=" CA  SER C 196 "
           pdb=" C   SER C 196 "
           pdb=" N   ILE C 197 "
           pdb=" CA  ILE C 197 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.94   29.06     0      5.00e+00 4.00e-02 3.38e+01
  dihedral pdb=" CA  ASN A 109 "
           pdb=" C   ASN A 109 "
           pdb=" N   ILE A 110 "
           pdb=" CA  ILE A 110 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.97  -23.03     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  SER A 184 "
           pdb=" C   SER A 184 "
           pdb=" N   HIS A 185 "
           pdb=" CA  HIS A 185 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.46  -21.54     0      5.00e+00 4.00e-02 1.86e+01
  ... (remaining 8201 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1771
       0.056 -    0.112: 271
       0.112 -    0.168: 29
       0.168 -    0.224: 2
       0.224 -    0.280: 1
  Chirality restraints: 2074
  Sorted by residual:
  chirality pdb=" CB  ILE B 112 "
            pdb=" CA  ILE B 112 "
            pdb=" CG1 ILE B 112 "
            pdb=" CG2 ILE B 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" CG  LEU A 546 "
            pdb=" CB  LEU A 546 "
            pdb=" CD1 LEU A 546 "
            pdb=" CD2 LEU A 546 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CG  LEU A 737 "
            pdb=" CB  LEU A 737 "
            pdb=" CD1 LEU A 737 "
            pdb=" CD2 LEU A 737 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.59e-01
  ... (remaining 2071 not shown)

  Planarity restraints: 2240
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B  45 "   -0.031 5.00e-02 4.00e+02   4.77e-02 3.63e+00
        pdb=" N   PRO B  46 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO B  46 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B  46 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 592 "    0.030 5.00e-02 4.00e+02   4.49e-02 3.23e+00
        pdb=" N   PRO A 593 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 593 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 593 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT P  17 "    0.021 2.00e-02 2.50e+03   1.01e-02 2.57e+00
        pdb=" N1   DT P  17 "   -0.021 2.00e-02 2.50e+03
        pdb=" C2   DT P  17 "   -0.003 2.00e-02 2.50e+03
        pdb=" O2   DT P  17 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3   DT P  17 "    0.003 2.00e-02 2.50e+03
        pdb=" C4   DT P  17 "    0.005 2.00e-02 2.50e+03
        pdb=" O4   DT P  17 "    0.006 2.00e-02 2.50e+03
        pdb=" C5   DT P  17 "    0.002 2.00e-02 2.50e+03
        pdb=" C7   DT P  17 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6   DT P  17 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 2237 not shown)

  Histogram of nonbonded interaction distances:
        1.85 -     2.46: 66
        2.46 -     3.07: 8892
        3.07 -     3.68: 20530
        3.68 -     4.29: 29642
        4.29 -     4.90: 48432
  Nonbonded interactions: 107562
  Sorted by model distance:
  nonbonded pdb="CA    CA A1102 "
            pdb="CA    CA A1103 "
     model   vdw
     1.849 1.980
  nonbonded pdb=" O   GLU A 879 "
            pdb=" OH  TYR A 968 "
     model   vdw
     2.074 3.040
  nonbonded pdb=" O   ASN A 181 "
            pdb=" OH  TYR A 271 "
     model   vdw
     2.123 3.040
  nonbonded pdb=" OH  TYR A 332 "
            pdb=" OE1 GLU A 926 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OH  TYR A 162 "
            pdb=" OE1 GLU A 476 "
     model   vdw
     2.259 3.040
  ... (remaining 107557 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.550
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     33.220
  Find NCS groups from input model:        0.130
  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:             0.010
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6006
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      :  0.002   0.050  13707  Z= 0.111
  Angle     :  0.520   7.185  18647  Z= 0.282
  Chirality :  0.041   0.280   2074
  Planarity :  0.004   0.048   2240
  Dihedral  : 16.998 178.214   5236
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.22), residues: 1518
  helix:  1.07 (0.24), residues: 488
  sheet: -0.52 (0.38), residues: 219
  loop : -2.46 (0.21), residues: 811

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 212 
 HIS   0.001   0.000   HIS A  36 
 PHE   0.020   0.001   PHE A 673 
 TYR   0.010   0.001   TYR A 658 
 ARG   0.003   0.000   ARG A  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15743 (  411)
  hydrogen bonds       : angle       5.87247 ( 1173)
  covalent geometry    : bond        0.00239 (13707)
  covalent geometry    : angle       0.52020 (18647)

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

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

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 278
  time to evaluate  : 1.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 SER cc_start: 0.8437 (m) cc_final: 0.8080 (m)
REVERT: A  215 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7183 (tm-30)
REVERT: A  374 ASP cc_start: 0.7372 (m-30) cc_final: 0.7166 (t0)
REVERT: A  435 LYS cc_start: 0.7945 (ptpp) cc_final: 0.7192 (tptt)
REVERT: A  525 LYS cc_start: 0.5422 (tptp) cc_final: 0.5173 (tptp)
REVERT: A  539 LYS cc_start: 0.6881 (ttmt) cc_final: 0.6623 (ttmt)
REVERT: A  668 TYR cc_start: 0.7115 (t80) cc_final: 0.6847 (t80)
REVERT: A  844 LYS cc_start: 0.6512 (mtmt) cc_final: 0.5656 (ttmm)
REVERT: A  909 TYR cc_start: 0.6059 (m-80) cc_final: 0.5778 (m-80)
REVERT: A  993 PHE cc_start: 0.7632 (m-80) cc_final: 0.7387 (m-80)
REVERT: C  243 LYS cc_start: 0.7844 (mttm) cc_final: 0.7488 (ttpp)
REVERT: C  297 ILE cc_start: 0.6932 (mm) cc_final: 0.6705 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 278
  average time/residue: 0.2719
  time to fit residues: 107.0519
Evaluate side-chains
  172 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 1.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 132 optimal weight:    0.0040
   chunk 118 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 80 optimal weight:    4.9990
   chunk 63 optimal weight:    0.0050
   chunk 123 optimal weight:    9.9990
   chunk 47 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0670
   chunk 91 optimal weight:    0.6980
   chunk 142 optimal weight:    5.9990
   overall best weight:    0.3144

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

Flipped N/Q/H residues before XYZ refinement:
A 322 ASN
A 442 GLN
A 897 HIS
A 994 GLN
B 120 ASN
** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 252 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4917 r_free = 0.4917 target = 0.234063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.195856 restraints weight = 16117.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.4576 rms_B_bonded: 2.60
r_work: 0.4326 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.4326
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4324
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4324 r_free = 0.4324    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4324 r_free = 0.4324    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
r_final: 0.4324
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6257
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  13707  Z= 0.126
  Angle     :  0.593   7.265  18647  Z= 0.313
  Chirality :  0.042   0.191   2074
  Planarity :  0.005   0.065   2240
  Dihedral  : 16.415 179.714   2088
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  :  9.21 %
    Favored  : 89.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.22), residues: 1518
  helix:  0.80 (0.24), residues: 503
  sheet: -0.66 (0.37), residues: 222
  loop : -2.56 (0.21), residues: 793

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 119 
 HIS   0.008   0.001   HIS B 187 
 PHE   0.016   0.001   PHE C 272 
 TYR   0.028   0.001   TYR A 486 
 ARG   0.004   0.000   ARG B 193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04060 (  411)
  hydrogen bonds       : angle       5.11359 ( 1173)
  covalent geometry    : bond        0.00279 (13707)
  covalent geometry    : angle       0.59291 (18647)

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

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

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 193
  time to evaluate  : 1.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 MET cc_start: 0.3851 (mpp) cc_final: 0.3610 (mpp)
REVERT: A  374 ASP cc_start: 0.7332 (m-30) cc_final: 0.7080 (t0)
REVERT: A  435 LYS cc_start: 0.7946 (ptpp) cc_final: 0.7183 (tptt)
REVERT: A  525 LYS cc_start: 0.5651 (tptp) cc_final: 0.5238 (tptp)
REVERT: A  620 GLU cc_start: 0.7467 (mp0) cc_final: 0.7061 (tt0)
REVERT: A  668 TYR cc_start: 0.7062 (t80) cc_final: 0.6781 (t80)
REVERT: A  741 TYR cc_start: 0.5840 (m-80) cc_final: 0.5164 (m-80)
REVERT: A  844 LYS cc_start: 0.6465 (mtmt) cc_final: 0.5512 (ttmm)
REVERT: A  899 ASN cc_start: 0.6412 (OUTLIER) cc_final: 0.6173 (p0)
REVERT: C  243 LYS cc_start: 0.8298 (mttm) cc_final: 0.7564 (ttpp)
  outliers start: 18
  outliers final: 11
  residues processed: 209
  average time/residue: 0.2475
  time to fit residues: 75.9493
Evaluate side-chains
  172 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 160
  time to evaluate  : 1.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  432 SER
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  804 LYS
Chi-restraints excluded: chain A residue  850 LEU
Chi-restraints excluded: chain A residue  899 ASN
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain C residue  142 ILE
Chi-restraints excluded: chain C residue  339 ASN
Chi-restraints excluded: chain C residue  392 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 145 optimal weight:    0.9990
   chunk 150 optimal weight:    0.0670
   chunk 111 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 116 optimal weight:    7.9990
   chunk 19 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 127 optimal weight:    5.9990
   chunk 80 optimal weight:    4.9990
   chunk 112 optimal weight:    0.9990
   overall best weight:    0.9324

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
A 181 ASN
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 252 HIS
C 409 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4859 r_free = 0.4859 target = 0.226713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.188540 restraints weight = 16233.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.4516 rms_B_bonded: 2.58
r_work: 0.4255 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.4255
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4253
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4253 r_free = 0.4253    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4252 r_free = 0.4252    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
r_final: 0.4252
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6398
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  13707  Z= 0.158
  Angle     :  0.609   7.946  18647  Z= 0.322
  Chirality :  0.043   0.213   2074
  Planarity :  0.005   0.059   2240
  Dihedral  : 16.495 179.657   2088
  Min Nonbonded Distance : 1.793

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.13 %
    Favored  : 88.87 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 13.75 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.22), residues: 1518
  helix:  0.53 (0.23), residues: 505
  sheet: -0.74 (0.37), residues: 219
  loop : -2.61 (0.21), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A   8 
 HIS   0.006   0.001   HIS C 252 
 PHE   0.022   0.002   PHE A 328 
 TYR   0.020   0.002   TYR A 486 
 ARG   0.003   0.000   ARG A 634 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04020 (  411)
  hydrogen bonds       : angle       5.23225 ( 1173)
  covalent geometry    : bond        0.00371 (13707)
  covalent geometry    : angle       0.60861 (18647)

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

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

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 180
  time to evaluate  : 1.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  374 ASP cc_start: 0.7372 (m-30) cc_final: 0.7093 (t0)
REVERT: A  525 LYS cc_start: 0.5722 (tptp) cc_final: 0.5341 (tptp)
REVERT: A  620 GLU cc_start: 0.7527 (mp0) cc_final: 0.7118 (tt0)
REVERT: A  668 TYR cc_start: 0.7128 (t80) cc_final: 0.6876 (t80)
REVERT: A  741 TYR cc_start: 0.5974 (m-80) cc_final: 0.5389 (m-80)
REVERT: C  100 SER cc_start: 0.7288 (m) cc_final: 0.7065 (t)
REVERT: C  219 TYR cc_start: 0.6971 (t80) cc_final: 0.6186 (t80)
REVERT: C  243 LYS cc_start: 0.8363 (mttm) cc_final: 0.7550 (ttpp)
REVERT: C  297 ILE cc_start: 0.6814 (mm) cc_final: 0.6570 (mp)
  outliers start: 26
  outliers final: 20
  residues processed: 199
  average time/residue: 0.2476
  time to fit residues: 71.9505
Evaluate side-chains
  174 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 154
  time to evaluate  : 1.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  432 SER
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  597 ILE
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  850 LEU
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  339 ASN
Chi-restraints excluded: chain C residue  392 THR
Chi-restraints excluded: chain C residue  402 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 148 optimal weight:    1.9990
   chunk 153 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   chunk 110 optimal weight:    2.9990
   chunk 140 optimal weight:   10.0000
   chunk 58 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 336 GLN
A 352 ASN
A 461 HIS
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   8 HIS
B 133 HIS
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 164 ASN
C 252 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4781 r_free = 0.4781 target = 0.217349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.178343 restraints weight = 16439.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.4391 rms_B_bonded: 2.53
r_work: 0.4103 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.4103
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4131
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4131 r_free = 0.4131    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4130 r_free = 0.4130    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
r_final: 0.4130
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6694
moved from start:          0.3180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.088  13707  Z= 0.302
  Angle     :  0.786   9.666  18647  Z= 0.417
  Chirality :  0.049   0.192   2074
  Planarity :  0.006   0.068   2240
  Dihedral  : 16.899 178.241   2088
  Min Nonbonded Distance : 1.721

Molprobity Statistics.
  All-atom Clashscore : 19.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.50 %
    Favored  : 86.50 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 16.75 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.21), residues: 1518
  helix: -0.45 (0.22), residues: 509
  sheet: -1.20 (0.37), residues: 225
  loop : -2.97 (0.20), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A   8 
 HIS   0.011   0.002   HIS B 133 
 PHE   0.038   0.003   PHE A 930 
 TYR   0.031   0.003   TYR A 909 
 ARG   0.008   0.001   ARG A 223 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05535 (  411)
  hydrogen bonds       : angle       6.17632 ( 1173)
  covalent geometry    : bond        0.00717 (13707)
  covalent geometry    : angle       0.78606 (18647)

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

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

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 186
  time to evaluate  : 1.638 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5459 (pm20)
REVERT: A  140 TYR cc_start: 0.5585 (m-10) cc_final: 0.5027 (m-80)
REVERT: A  165 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7900 (pp)
REVERT: A  374 ASP cc_start: 0.7533 (m-30) cc_final: 0.7078 (t0)
REVERT: A  525 LYS cc_start: 0.5876 (tptp) cc_final: 0.5479 (tptp)
REVERT: A  620 GLU cc_start: 0.7741 (mp0) cc_final: 0.7240 (tt0)
REVERT: A  833 ARG cc_start: 0.6996 (tpm170) cc_final: 0.6657 (tpm170)
REVERT: A  853 MET cc_start: 0.7117 (ttp) cc_final: 0.6811 (mtm)
REVERT: B   23 MET cc_start: 0.4640 (tmm) cc_final: 0.4324 (tmm)
REVERT: B  203 GLU cc_start: 0.6490 (tp30) cc_final: 0.6108 (tp30)
REVERT: C  219 TYR cc_start: 0.6918 (t80) cc_final: 0.5975 (t80)
REVERT: C  243 LYS cc_start: 0.8303 (mttm) cc_final: 0.7572 (ttpp)
  outliers start: 49
  outliers final: 29
  residues processed: 226
  average time/residue: 0.2495
  time to fit residues: 83.6672
Evaluate side-chains
  198 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 167
  time to evaluate  : 1.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue  106 GLU
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  432 SER
Chi-restraints excluded: chain A residue  436 ASP
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  566 GLU
Chi-restraints excluded: chain A residue  597 ILE
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  648 THR
Chi-restraints excluded: chain A residue  757 THR
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  844 LYS
Chi-restraints excluded: chain A residue  850 LEU
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  181 HIS
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  339 ASN
Chi-restraints excluded: chain C residue  392 THR
Chi-restraints excluded: chain C residue  402 THR
Chi-restraints excluded: chain C residue  424 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 142 optimal weight:    6.9990
   chunk 140 optimal weight:    3.9990
   chunk 131 optimal weight:   20.0000
   chunk 102 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 152 optimal weight:    1.9990
   chunk 155 optimal weight:    4.9990
   chunk 27 optimal weight:    0.2980
   chunk 45 optimal weight:    0.9990
   chunk 119 optimal weight:    0.8980
   chunk 146 optimal weight:    0.9990
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 825 ASN
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 187 HIS
C 164 ASN
C 252 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4805 r_free = 0.4805 target = 0.220239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.181507 restraints weight = 16313.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.4426 rms_B_bonded: 2.40
r_work: 0.4164 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4173
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4173 r_free = 0.4173    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4173 r_free = 0.4173    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
r_final: 0.4173
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6526
moved from start:          0.3225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  13707  Z= 0.172
  Angle     :  0.651   8.504  18647  Z= 0.345
  Chirality :  0.044   0.183   2074
  Planarity :  0.005   0.057   2240
  Dihedral  : 16.704 177.677   2088
  Min Nonbonded Distance : 1.804

Molprobity Statistics.
  All-atom Clashscore : 15.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.66 %
    Favored  : 88.34 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 18.84 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.41 (0.21), residues: 1518
  helix:  0.00 (0.23), residues: 497
  sheet: -1.37 (0.37), residues: 220
  loop : -2.84 (0.20), residues: 801

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A   8 
 HIS   0.007   0.001   HIS C 252 
 PHE   0.018   0.002   PHE A 113 
 TYR   0.025   0.002   TYR A 928 
 ARG   0.007   0.001   ARG A 781 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04299 (  411)
  hydrogen bonds       : angle       5.69453 ( 1173)
  covalent geometry    : bond        0.00405 (13707)
  covalent geometry    : angle       0.65112 (18647)

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

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

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 169
  time to evaluate  : 1.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 MET cc_start: 0.4072 (mpp) cc_final: 0.3633 (mpp)
REVERT: A  106 GLU cc_start: 0.5788 (OUTLIER) cc_final: 0.4934 (pm20)
REVERT: A  165 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.8011 (pp)
REVERT: A  357 MET cc_start: 0.3596 (mtt) cc_final: 0.2963 (mmt)
REVERT: A  374 ASP cc_start: 0.7485 (m-30) cc_final: 0.7091 (t0)
REVERT: A  525 LYS cc_start: 0.5710 (tptp) cc_final: 0.5253 (tptp)
REVERT: A  620 GLU cc_start: 0.7659 (mp0) cc_final: 0.7047 (tt0)
REVERT: A  833 ARG cc_start: 0.6837 (tpm170) cc_final: 0.6451 (tpm170)
REVERT: A  853 MET cc_start: 0.7048 (ttp) cc_final: 0.6715 (mtm)
REVERT: A  926 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.4766 (pp20)
REVERT: B   23 MET cc_start: 0.4705 (tmm) cc_final: 0.4403 (tmm)
REVERT: B  203 GLU cc_start: 0.6405 (tp30) cc_final: 0.5974 (tp30)
REVERT: C  138 MET cc_start: 0.7682 (ptp) cc_final: 0.7333 (ptt)
REVERT: C  200 ILE cc_start: 0.4613 (mp) cc_final: 0.4264 (mt)
REVERT: C  219 TYR cc_start: 0.6885 (t80) cc_final: 0.5944 (t80)
REVERT: C  243 LYS cc_start: 0.8316 (mttm) cc_final: 0.7577 (ttpp)
  outliers start: 46
  outliers final: 30
  residues processed: 202
  average time/residue: 0.2435
  time to fit residues: 73.0950
Evaluate side-chains
  193 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 160
  time to evaluate  : 1.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  106 GLU
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  231 ASP
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  432 SER
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  566 GLU
Chi-restraints excluded: chain A residue  597 ILE
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  757 THR
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  844 LYS
Chi-restraints excluded: chain A residue  899 ASN
Chi-restraints excluded: chain A residue  926 GLU
Chi-restraints excluded: chain A residue  972 PHE
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  187 HIS
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  301 TYR
Chi-restraints excluded: chain C residue  339 ASN
Chi-restraints excluded: chain C residue  392 THR
Chi-restraints excluded: chain C residue  402 THR
Chi-restraints excluded: chain C residue  424 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 72 optimal weight:    0.0980
   chunk 136 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0770
   chunk 45 optimal weight:    0.9980
   chunk 152 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 118 optimal weight:    0.4980
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
A 307 HIS
A 322 ASN
C 252 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4843 r_free = 0.4843 target = 0.224385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.186173 restraints weight = 16588.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.4477 rms_B_bonded: 2.58
r_work: 0.4222 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.4222
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4250
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4250 r_free = 0.4250    target_work(ls_wunit_k1) = 0.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4250 r_free = 0.4250    target_work(ls_wunit_k1) = 0.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
r_final: 0.4250
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6416
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  13707  Z= 0.128
  Angle     :  0.604   7.904  18647  Z= 0.319
  Chirality :  0.042   0.199   2074
  Planarity :  0.004   0.059   2240
  Dihedral  : 16.534 177.774   2088
  Min Nonbonded Distance : 1.851

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.20 %
    Favored  : 88.80 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 19.89 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.21), residues: 1518
  helix:  0.28 (0.23), residues: 495
  sheet: -1.10 (0.36), residues: 224
  loop : -2.72 (0.21), residues: 799

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 136 
 HIS   0.021   0.001   HIS B 187 
 PHE   0.037   0.001   PHE A 113 
 TYR   0.028   0.001   TYR A 928 
 ARG   0.006   0.000   ARG A 634 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03609 (  411)
  hydrogen bonds       : angle       5.36772 ( 1173)
  covalent geometry    : bond        0.00288 (13707)
  covalent geometry    : angle       0.60422 (18647)

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

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

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 169
  time to evaluate  : 1.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 GLU cc_start: 0.5812 (OUTLIER) cc_final: 0.4787 (pm20)
REVERT: A  203 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7949 (mt)
REVERT: A  374 ASP cc_start: 0.7448 (m-30) cc_final: 0.7052 (t0)
REVERT: A  471 GLU cc_start: 0.5901 (mt-10) cc_final: 0.5425 (mt-10)
REVERT: A  525 LYS cc_start: 0.5482 (tptp) cc_final: 0.4968 (tptp)
REVERT: A  620 GLU cc_start: 0.7614 (mp0) cc_final: 0.7004 (tt0)
REVERT: B   23 MET cc_start: 0.4818 (tmm) cc_final: 0.4550 (tmm)
REVERT: C  100 SER cc_start: 0.7130 (m) cc_final: 0.6862 (t)
REVERT: C  138 MET cc_start: 0.7584 (ptp) cc_final: 0.7180 (ptt)
REVERT: C  219 TYR cc_start: 0.6853 (t80) cc_final: 0.5924 (t80)
REVERT: C  243 LYS cc_start: 0.8304 (mttm) cc_final: 0.7799 (ttpp)
  outliers start: 42
  outliers final: 25
  residues processed: 202
  average time/residue: 0.2278
  time to fit residues: 69.8035
Evaluate side-chains
  179 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 152
  time to evaluate  : 1.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 GLU
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  566 GLU
Chi-restraints excluded: chain A residue  597 ILE
Chi-restraints excluded: chain A residue  648 THR
Chi-restraints excluded: chain A residue  757 THR
Chi-restraints excluded: chain A residue  844 LYS
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  972 PHE
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  339 ASN
Chi-restraints excluded: chain C residue  392 THR
Chi-restraints excluded: chain C residue  402 THR
Chi-restraints excluded: chain C residue  424 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 117 optimal weight:    6.9990
   chunk 146 optimal weight:    0.6980
   chunk 123 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 150 optimal weight:    4.9990
   chunk 70 optimal weight:    0.8980
   chunk 114 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 187 HIS
C 115 ASN
C 164 ASN
C 252 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4824 r_free = 0.4824 target = 0.222333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.184344 restraints weight = 16450.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.4460 rms_B_bonded: 2.56
r_work: 0.4188 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.4188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4215
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4215 r_free = 0.4215    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4215 r_free = 0.4215    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
r_final: 0.4215
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6489
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  13707  Z= 0.159
  Angle     :  0.640   9.040  18647  Z= 0.336
  Chirality :  0.044   0.255   2074
  Planarity :  0.005   0.060   2240
  Dihedral  : 16.565 177.861   2088
  Min Nonbonded Distance : 1.801

Molprobity Statistics.
  All-atom Clashscore : 14.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.06 %
    Favored  : 87.94 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 20.38 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.21), residues: 1518
  helix:  0.08 (0.23), residues: 501
  sheet: -1.17 (0.37), residues: 216
  loop : -2.75 (0.21), residues: 801

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 136 
 HIS   0.007   0.001   HIS C 252 
 PHE   0.023   0.002   PHE A 113 
 TYR   0.021   0.002   TYR A 928 
 ARG   0.006   0.000   ARG A 634 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04001 (  411)
  hydrogen bonds       : angle       5.45868 ( 1173)
  covalent geometry    : bond        0.00371 (13707)
  covalent geometry    : angle       0.63971 (18647)

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

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

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 163
  time to evaluate  : 1.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 GLU cc_start: 0.5867 (OUTLIER) cc_final: 0.4879 (pm20)
REVERT: A  200 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6036 (m-80)
REVERT: A  203 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7996 (mt)
REVERT: A  374 ASP cc_start: 0.7452 (m-30) cc_final: 0.7063 (t0)
REVERT: A  525 LYS cc_start: 0.5615 (tptp) cc_final: 0.5081 (tptp)
REVERT: A  529 GLU cc_start: 0.3272 (OUTLIER) cc_final: 0.2130 (tp30)
REVERT: A  620 GLU cc_start: 0.7659 (mp0) cc_final: 0.7078 (tt0)
REVERT: A  801 GLN cc_start: 0.6781 (OUTLIER) cc_final: 0.6517 (mt0)
REVERT: A  926 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.4605 (pp20)
REVERT: B   23 MET cc_start: 0.4815 (tmm) cc_final: 0.4568 (tmm)
REVERT: C  100 SER cc_start: 0.7140 (m) cc_final: 0.6899 (t)
REVERT: C  138 MET cc_start: 0.7570 (ptp) cc_final: 0.7135 (ptt)
REVERT: C  164 ASN cc_start: 0.3085 (OUTLIER) cc_final: 0.2880 (m-40)
REVERT: C  219 TYR cc_start: 0.6842 (t80) cc_final: 0.5930 (t80)
REVERT: C  243 LYS cc_start: 0.8364 (mttm) cc_final: 0.7869 (ttpp)
  outliers start: 52
  outliers final: 37
  residues processed: 204
  average time/residue: 0.2360
  time to fit residues: 72.8485
Evaluate side-chains
  198 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 154
  time to evaluate  : 1.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  106 GLU
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  432 SER
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  529 GLU
Chi-restraints excluded: chain A residue  597 ILE
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  648 THR
Chi-restraints excluded: chain A residue  757 THR
Chi-restraints excluded: chain A residue  758 GLU
Chi-restraints excluded: chain A residue  801 GLN
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  844 LYS
Chi-restraints excluded: chain A residue  899 ASN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  926 GLU
Chi-restraints excluded: chain A residue  972 PHE
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  181 HIS
Chi-restraints excluded: chain B residue  187 HIS
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  164 ASN
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  200 ILE
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  301 TYR
Chi-restraints excluded: chain C residue  339 ASN
Chi-restraints excluded: chain C residue  392 THR
Chi-restraints excluded: chain C residue  402 THR
Chi-restraints excluded: chain C residue  424 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 67 optimal weight:    0.8980
   chunk 109 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   chunk 87 optimal weight:    0.8980
   chunk 88 optimal weight:    0.0070
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 164 ASN
C 252 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4826 r_free = 0.4826 target = 0.223159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.184990 restraints weight = 16519.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.4451 rms_B_bonded: 2.58
r_work: 0.4191 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.4191
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4227
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4227 r_free = 0.4227    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4227 r_free = 0.4227    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
r_final: 0.4227
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6446
moved from start:          0.3440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  13707  Z= 0.144
  Angle     :  0.632  11.534  18647  Z= 0.331
  Chirality :  0.043   0.217   2074
  Planarity :  0.005   0.060   2240
  Dihedral  : 16.528 177.756   2088
  Min Nonbonded Distance : 1.824

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 11.40 %
    Favored  : 88.54 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 20.73 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.21), residues: 1518
  helix:  0.21 (0.23), residues: 491
  sheet: -1.22 (0.36), residues: 227
  loop : -2.68 (0.21), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 136 
 HIS   0.018   0.001   HIS B 187 
 PHE   0.033   0.001   PHE A 113 
 TYR   0.029   0.002   TYR A 928 
 ARG   0.007   0.000   ARG A 634 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03737 (  411)
  hydrogen bonds       : angle       5.41127 ( 1173)
  covalent geometry    : bond        0.00333 (13707)
  covalent geometry    : angle       0.63184 (18647)

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

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

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 157
  time to evaluate  : 1.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 GLU cc_start: 0.5766 (OUTLIER) cc_final: 0.4730 (pm20)
REVERT: A  200 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.6099 (m-80)
REVERT: A  203 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7935 (mt)
REVERT: A  374 ASP cc_start: 0.7481 (m-30) cc_final: 0.7059 (t0)
REVERT: A  471 GLU cc_start: 0.5908 (mt-10) cc_final: 0.5491 (mt-10)
REVERT: A  525 LYS cc_start: 0.5494 (tptp) cc_final: 0.4963 (tptp)
REVERT: A  529 GLU cc_start: 0.3135 (OUTLIER) cc_final: 0.1967 (tp30)
REVERT: A  620 GLU cc_start: 0.7647 (mp0) cc_final: 0.7070 (tt0)
REVERT: A  801 GLN cc_start: 0.6730 (OUTLIER) cc_final: 0.6464 (mt0)
REVERT: A  926 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.4358 (pp20)
REVERT: B   23 MET cc_start: 0.4821 (tmm) cc_final: 0.4572 (tmm)
REVERT: C  100 SER cc_start: 0.7075 (m) cc_final: 0.6860 (t)
REVERT: C  138 MET cc_start: 0.7626 (ptp) cc_final: 0.7229 (ptt)
REVERT: C  219 TYR cc_start: 0.6864 (t80) cc_final: 0.5974 (t80)
REVERT: C  243 LYS cc_start: 0.8341 (mttm) cc_final: 0.7570 (tttp)
  outliers start: 48
  outliers final: 36
  residues processed: 195
  average time/residue: 0.2316
  time to fit residues: 68.4235
Evaluate side-chains
  195 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 153
  time to evaluate  : 1.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  106 GLU
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  432 SER
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  529 GLU
Chi-restraints excluded: chain A residue  597 ILE
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  648 THR
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  757 THR
Chi-restraints excluded: chain A residue  758 GLU
Chi-restraints excluded: chain A residue  768 ILE
Chi-restraints excluded: chain A residue  801 GLN
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  899 ASN
Chi-restraints excluded: chain A residue  926 GLU
Chi-restraints excluded: chain A residue  972 PHE
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  301 TYR
Chi-restraints excluded: chain C residue  339 ASN
Chi-restraints excluded: chain C residue  392 THR
Chi-restraints excluded: chain C residue  402 THR
Chi-restraints excluded: chain C residue  424 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 15 optimal weight:    0.0670
   chunk 9 optimal weight:    1.9990
   chunk 119 optimal weight:   10.0000
   chunk 100 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0030
   chunk 99 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   overall best weight:    0.5930

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

Flipped N/Q/H residues before XYZ refinement:
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 164 ASN
C 252 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4839 r_free = 0.4839 target = 0.224573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.186410 restraints weight = 16280.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.4467 rms_B_bonded: 2.46
r_work: 0.4218 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.4076 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.4076
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4110
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4110 r_free = 0.4110    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4110 r_free = 0.4110    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
r_final: 0.4110
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6548
moved from start:          0.3524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  13707  Z= 0.137
  Angle     :  0.621  11.363  18647  Z= 0.325
  Chirality :  0.042   0.221   2074
  Planarity :  0.004   0.062   2240
  Dihedral  : 16.487 177.846   2088
  Min Nonbonded Distance : 1.828

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 11.13 %
    Favored  : 88.80 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 20.87 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.22), residues: 1518
  helix:  0.29 (0.23), residues: 490
  sheet: -1.27 (0.35), residues: 227
  loop : -2.62 (0.21), residues: 801

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C 136 
 HIS   0.008   0.001   HIS C 252 
 PHE   0.017   0.001   PHE A 113 
 TYR   0.029   0.002   TYR A 928 
 ARG   0.007   0.000   ARG A 634 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03616 (  411)
  hydrogen bonds       : angle       5.33865 ( 1173)
  covalent geometry    : bond        0.00315 (13707)
  covalent geometry    : angle       0.62104 (18647)

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

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

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 161
  time to evaluate  : 1.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 GLU cc_start: 0.5750 (OUTLIER) cc_final: 0.4818 (pm20)
REVERT: A  200 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6155 (m-80)
REVERT: A  203 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8024 (mt)
REVERT: A  214 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.6848 (mp10)
REVERT: A  374 ASP cc_start: 0.7610 (m-30) cc_final: 0.7072 (t0)
REVERT: A  439 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7368 (p0)
REVERT: A  525 LYS cc_start: 0.5369 (tptp) cc_final: 0.4814 (tptp)
REVERT: A  529 GLU cc_start: 0.2972 (OUTLIER) cc_final: 0.1788 (tp30)
REVERT: A  620 GLU cc_start: 0.7827 (mp0) cc_final: 0.7099 (tt0)
REVERT: A  926 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.4397 (pp20)
REVERT: C  100 SER cc_start: 0.7211 (m) cc_final: 0.6973 (t)
REVERT: C  138 MET cc_start: 0.7771 (ptp) cc_final: 0.7363 (ptt)
REVERT: C  219 TYR cc_start: 0.6840 (t80) cc_final: 0.5936 (t80)
REVERT: C  243 LYS cc_start: 0.8344 (mttm) cc_final: 0.7573 (tttp)
  outliers start: 49
  outliers final: 35
  residues processed: 199
  average time/residue: 0.2384
  time to fit residues: 70.1907
Evaluate side-chains
  193 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 151
  time to evaluate  : 1.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  106 GLU
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  432 SER
Chi-restraints excluded: chain A residue  439 ASP
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  529 GLU
Chi-restraints excluded: chain A residue  597 ILE
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  648 THR
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  757 THR
Chi-restraints excluded: chain A residue  758 GLU
Chi-restraints excluded: chain A residue  768 ILE
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  899 ASN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  926 GLU
Chi-restraints excluded: chain A residue  972 PHE
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  301 TYR
Chi-restraints excluded: chain C residue  339 ASN
Chi-restraints excluded: chain C residue  392 THR
Chi-restraints excluded: chain C residue  402 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 137 optimal weight:   10.0000
   chunk 77 optimal weight:    0.7980
   chunk 110 optimal weight:    0.7980
   chunk 70 optimal weight:    7.9990
   chunk 129 optimal weight:    7.9990
   chunk 130 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 145 optimal weight:    0.6980
   chunk 120 optimal weight:    0.0570
   chunk 65 optimal weight:    3.9990
   overall best weight:    1.0700

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

Flipped N/Q/H residues before XYZ refinement:
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 164 ASN
C 252 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4808 r_free = 0.4808 target = 0.221397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.182796 restraints weight = 16456.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.4433 rms_B_bonded: 2.67
r_work: 0.4163 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.4163
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4190 r_free = 0.4190    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4190 r_free = 0.4190    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
r_final: 0.4190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6522
moved from start:          0.3688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  13707  Z= 0.176
  Angle     :  0.653  10.676  18647  Z= 0.344
  Chirality :  0.044   0.225   2074
  Planarity :  0.005   0.062   2240
  Dihedral  : 16.568 177.804   2088
  Min Nonbonded Distance : 1.782

Molprobity Statistics.
  All-atom Clashscore : 14.46
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 11.99 %
    Favored  : 87.94 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.14 %
    Favored  : 75.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.21), residues: 1518
  helix: -0.01 (0.23), residues: 498
  sheet: -1.45 (0.35), residues: 226
  loop : -2.74 (0.21), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP C 136 
 HIS   0.008   0.001   HIS C 252 
 PHE   0.027   0.002   PHE A 930 
 TYR   0.025   0.002   TYR A 909 
 ARG   0.011   0.001   ARG A 849 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04087 (  411)
  hydrogen bonds       : angle       5.54846 ( 1173)
  covalent geometry    : bond        0.00416 (13707)
  covalent geometry    : angle       0.65330 (18647)

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

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

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3036 Ramachandran restraints generated.
    1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 156
  time to evaluate  : 1.665 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 GLU cc_start: 0.5838 (OUTLIER) cc_final: 0.4931 (pm20)
REVERT: A  200 PHE cc_start: 0.7176 (OUTLIER) cc_final: 0.6066 (m-80)
REVERT: A  203 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7999 (mt)
REVERT: A  374 ASP cc_start: 0.7576 (m-30) cc_final: 0.7126 (t0)
REVERT: A  439 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7160 (p0)
REVERT: A  525 LYS cc_start: 0.5570 (tptp) cc_final: 0.5013 (tptp)
REVERT: A  620 GLU cc_start: 0.7711 (mp0) cc_final: 0.7154 (tt0)
REVERT: A  801 GLN cc_start: 0.6854 (OUTLIER) cc_final: 0.6575 (mt0)
REVERT: A  853 MET cc_start: 0.7140 (mtp) cc_final: 0.6766 (mtm)
REVERT: A  926 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.4346 (pp20)
REVERT: C  100 SER cc_start: 0.7225 (m) cc_final: 0.6979 (t)
REVERT: C  138 MET cc_start: 0.7572 (ptp) cc_final: 0.7177 (ptt)
REVERT: C  219 TYR cc_start: 0.6880 (t80) cc_final: 0.5907 (t80)
REVERT: C  243 LYS cc_start: 0.8334 (mttm) cc_final: 0.7580 (tttp)
  outliers start: 47
  outliers final: 34
  residues processed: 193
  average time/residue: 0.2326
  time to fit residues: 67.9870
Evaluate side-chains
  192 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 152
  time to evaluate  : 1.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue  106 GLU
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  432 SER
Chi-restraints excluded: chain A residue  439 ASP
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  529 GLU
Chi-restraints excluded: chain A residue  597 ILE
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  648 THR
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  757 THR
Chi-restraints excluded: chain A residue  758 GLU
Chi-restraints excluded: chain A residue  768 ILE
Chi-restraints excluded: chain A residue  801 GLN
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  899 ASN
Chi-restraints excluded: chain A residue  926 GLU
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  202 LEU
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  301 TYR
Chi-restraints excluded: chain C residue  339 ASN
Chi-restraints excluded: chain C residue  392 THR
Chi-restraints excluded: chain C residue  402 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 137 optimal weight:    0.0770
   chunk 34 optimal weight:    2.9990
   chunk 128 optimal weight:   10.0000
   chunk 110 optimal weight:    0.8980
   chunk 91 optimal weight:    0.0870
   chunk 31 optimal weight:    0.5980
   chunk 61 optimal weight:    0.5980
   chunk 75 optimal weight:    0.5980
   chunk 121 optimal weight:    4.9990
   chunk 143 optimal weight:   10.0000
   chunk 117 optimal weight:    6.9990
   overall best weight:    0.3916

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

Flipped N/Q/H residues before XYZ refinement:
C 164 ASN
C 252 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4856 r_free = 0.4856 target = 0.226247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.188633 restraints weight = 16310.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.4496 rms_B_bonded: 2.50
r_work: 0.4253 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.4253
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4283
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4283 r_free = 0.4283    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4283 r_free = 0.4283    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
r_final: 0.4283
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6363
moved from start:          0.3709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13707  Z= 0.127
  Angle     :  0.614  10.965  18647  Z= 0.322
  Chirality :  0.042   0.223   2074
  Planarity :  0.004   0.063   2240
  Dihedral  : 16.467 177.685   2088
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 10.28 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 21.70 %
    Favored  : 75.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.21), residues: 1518
  helix:  0.22 (0.23), residues: 497
  sheet: -1.49 (0.35), residues: 230
  loop : -2.60 (0.21), residues: 791

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C 136 
 HIS   0.008   0.001   HIS C 252 
 PHE   0.015   0.001   PHE A 930 
 TYR   0.019   0.001   TYR A 928 
 ARG   0.013   0.000   ARG A 849 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03500 (  411)
  hydrogen bonds       : angle       5.29255 ( 1173)
  covalent geometry    : bond        0.00289 (13707)
  covalent geometry    : angle       0.61367 (18647)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8738.51 seconds
wall clock time: 151 minutes 46.71 seconds (9106.71 seconds total)