Starting phenix.real_space_refine
on Fri Jul  3 12:13:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hpa_34929/07_2026/8hpa_34929.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hpa_34929/07_2026/8hpa_34929.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hpa_34929/07_2026/8hpa_34929.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hpa_34929/07_2026/8hpa_34929.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hpa_34929/07_2026/8hpa_34929.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hpa_34929/07_2026/8hpa_34929.cif"
  }
  resolution = 3.01
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.020
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: 5
    Type Number    sf(0)   Gaussians
     P      32      5.49       5
     S      72      5.16       5
     C    8943      2.51       5
     N    2353      2.21       5
     O    2722      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14122
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 8208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1004, 8208
          Classifications: {'peptide': 1004}
          Link IDs: {'CIS': 1, 'PTRANS': 37, 'TRANS': 965}
    Chain: "C"
      Number of atoms: 3467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3467
          Classifications: {'peptide': 426}
          Link IDs: {'PTRANS': 10, 'TRANS': 415}
    Chain: "B"
      Number of atoms: 1772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1772
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 13, 'TRANS': 204}
    Chain: "E"
      Number of atoms: 382
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 382
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
    Chain: "D"
      Number of atoms: 293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 293
          Classifications: {'DNA': 15}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 14}
  Residues with excluded nonbonded symmetry interactions: 31
    residue:
      pdb=" N   GLU A 856 " occ=0.41
      ... (7 atoms not shown)
      pdb=" OE2 GLU A 856 " occ=0.41
    residue:
      pdb=" N   GLY A 857 " occ=0.41
      ... (2 atoms not shown)
      pdb=" O   GLY A 857 " occ=0.41
    residue:
      pdb=" N   ARG A 858 " occ=0.32
      ... (9 atoms not shown)
      pdb=" NH2 ARG A 858 " occ=0.32
    residue:
      pdb=" N   MET A 859 " occ=0.42
      ... (6 atoms not shown)
      pdb=" CE  MET A 859 " occ=0.42
    residue:
      pdb=" N   ASN A 860 " occ=0.35
      ... (6 atoms not shown)
      pdb=" ND2 ASN A 860 " occ=0.35
    residue:
      pdb=" N   SER A 861 " occ=0.16
      ... (4 atoms not shown)
      pdb=" OG  SER A 861 " occ=0.16
    residue:
      pdb=" N   ASN A 862 " occ=0.26
      ... (6 atoms not shown)
      pdb=" ND2 ASN A 862 " occ=0.26
    residue:
      pdb=" N   GLN A 863 " occ=0.45
      ... (7 atoms not shown)
      pdb=" NE2 GLN A 863 " occ=0.45
    residue:
      pdb=" N   GLY C  46 " occ=0.88
      ... (2 atoms not shown)
      pdb=" O   GLY C  46 " occ=0.88
    residue:
      pdb=" N   VAL C  47 " occ=0.62
      ... (5 atoms not shown)
      pdb=" CG2 VAL C  47 " occ=0.62
    residue:
      pdb=" N   GLN C  48 " occ=0.77
      ... (7 atoms not shown)
      pdb=" NE2 GLN C  48 " occ=0.77
    residue:
      pdb=" N   LYS C  49 " occ=0.55
      ... (7 atoms not shown)
      pdb=" NZ  LYS C  49 " occ=0.55
    ... (remaining 19 not shown)
  Time building chain proxies: 2.31, per 1000 atoms: 0.16
  Number of scatterers: 14122
  At special positions: 0
  Unit cell: (113.4, 122.64, 143.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      72     16.00
     P      32     15.00
     O    2722      8.00
     N    2353      7.00
     C    8943      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: 0.88
  Conformation dependent library (CDL) restraints added in 485.2 milliseconds
  

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3154

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 15 sheets defined
      37.8% alpha, 14.0% beta
      1 base pairs and 18 stacking pairs defined.
    Time for finding SS restraints: 1.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 108 through 118
    Processing helix  chain 'A' and resid 144 through 149
      removed outlier: 3.645A  pdb=" N   CYS A 148 " --> pdb=" O   ASP A 144 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   PHE A 149 " --> pdb=" O   PRO A 145 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 144 through 149'
    Processing helix  chain 'A' and resid 209 through 219
    Processing helix  chain 'A' and resid 226 through 230
    Processing helix  chain 'A' and resid 240 through 253
    Processing helix  chain 'A' and resid 267 through 280
    Processing helix  chain 'A' and resid 331 through 339
    Processing helix  chain 'A' and resid 350 through 354
      removed outlier: 4.240A  pdb=" N   PHE A 354 " --> pdb=" O   LYS A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 390
      removed outlier: 3.641A  pdb=" N   THR A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 446
      removed outlier: 3.503A  pdb=" N   LYS A 445 " --> pdb=" O   ALA A 441 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ASP A 446 " --> pdb=" O   GLN A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 474
      removed outlier: 3.632A  pdb=" N   GLN A 467 " --> pdb=" O   ALA A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 486
    Processing helix  chain 'A' and resid 497 through 502
    Processing helix  chain 'A' and resid 502 through 514
    Processing helix  chain 'A' and resid 552 through 562
    Processing helix  chain 'A' and resid 576 through 591
      removed outlier: 3.743A  pdb=" N   GLN A 589 " --> pdb=" O   GLN A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 644
      removed outlier: 3.598A  pdb=" N   ARG A 625 " --> pdb=" O   GLY A 621 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 646 through 666
      removed outlier: 3.665A  pdb=" N   TYR A 658 " --> pdb=" O   ASP A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 672
      removed outlier: 3.821A  pdb=" N   GLY A 672 " --> pdb=" O   TYR A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 703
    Processing helix  chain 'A' and resid 764 through 782
    Processing helix  chain 'A' and resid 828 through 832
    Processing helix  chain 'A' and resid 837 through 856
      removed outlier: 3.676A  pdb=" N   ASN A 841 " --> pdb=" O   LYS A 837 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 879
    Processing helix  chain 'A' and resid 905 through 918
      removed outlier: 3.703A  pdb=" N   TYR A 914 " --> pdb=" O   LEU A 910 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 968 through 973
      removed outlier: 3.535A  pdb=" N   PHE A 972 " --> pdb=" O   TYR A 968 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LYS A 973 " --> pdb=" O   GLU A 969 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 968 through 973'
    Processing helix  chain 'A' and resid 973 through 981
    Processing helix  chain 'A' and resid 985 through 997
      removed outlier: 4.149A  pdb=" N   CYS A 989 " --> pdb=" O   ASN A 985 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 20
      removed outlier: 6.126A  pdb=" N   GLU C  12 " --> pdb=" O   THR C   8 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   LEU C  13 " --> pdb=" O   ASN C   9 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 23
      No H-bonds generated for 'chain 'C' and resid 21 through 23'
    Processing helix  chain 'C' and resid 24 through 39
    Processing helix  chain 'C' and resid 57 through 61
    Processing helix  chain 'C' and resid 108 through 115
    Processing helix  chain 'C' and resid 149 through 159
      removed outlier: 5.363A  pdb=" N   ALA C 155 " --> pdb=" O   ILE C 151 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   SER C 156 " --> pdb=" O   PHE C 152 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 177 through 189
      removed outlier: 3.651A  pdb=" N   ASP C 189 " --> pdb=" O   GLU C 185 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 298
    Processing helix  chain 'C' and resid 317 through 324
    Processing helix  chain 'C' and resid 330 through 341
    Processing helix  chain 'C' and resid 343 through 351
    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 426
    Processing helix  chain 'B' and resid 16 through 18
      No H-bonds generated for 'chain 'B' and resid 16 through 18'
    Processing helix  chain 'B' and resid 19 through 38
      removed outlier: 4.667A  pdb=" N   SER B  24 " --> pdb=" O   GLU B  20 " (cutoff:3.500A)
      removed outlier: 5.904A  pdb=" N   GLN B  25 " --> pdb=" O   PRO B  21 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   GLU B  32 " --> pdb=" O   GLU B  28 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   VAL B  33 " --> pdb=" O   PHE B  29 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   TRP B  36 " --> pdb=" O   GLU B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 49
    Processing helix  chain 'B' and resid 50 through 55
    Processing helix  chain 'B' and resid 86 through 101
    Processing helix  chain 'B' and resid 109 through 113
      removed outlier: 3.990A  pdb=" N   ILE B 112 " --> pdb=" O   ASN B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 150
      removed outlier: 5.284A  pdb=" N   LYS B 139 " --> pdb=" O   ILE B 135 " (cutoff:3.500A)
      removed outlier: 5.109A  pdb=" N   ILE B 140 " --> pdb=" O   TYR B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 204
      removed outlier: 3.554A  pdb=" N   VAL B 200 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126
      removed outlier: 5.587A  pdb=" N   CYS A   5 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   ARG A  23 " --> pdb=" O   CYS A   5 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASN A   7 " --> pdb=" O   LYS A  21 " (cutoff:3.500A)
      removed outlier: 8.403A  pdb=" N   TYR A 140 " --> pdb=" O   THR A  29 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   PHE A  31 " --> pdb=" O   TYR A 140 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   CYS A 142 " --> pdb=" O   PHE A  31 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   ARG A  33 " --> pdb=" O   CYS A 142 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ASN A 136 " --> pdb=" O   CYS A 139 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   HIS A 141 " --> pdb=" O   LYS A 134 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   LYS A 134 " --> pdb=" O   HIS A 141 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43
      removed outlier: 3.792A  pdb=" N   GLY A  61 " --> pdb=" O   MET A  88 " (cutoff:3.500A)
      removed outlier: 5.654A  pdb=" N   LEU A  90 " --> pdb=" O   PRO A  59 " (cutoff:3.500A)
      removed outlier: 7.340A  pdb=" N   GLU A  92 " --> pdb=" O   ALA A  57 " (cutoff:3.500A)
      removed outlier: 5.941A  pdb=" N   ALA A  57 " --> pdb=" O   GLU A  92 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73
      removed outlier: 6.018A  pdb=" N   SER A  73 " --> pdb=" O   VAL A 573 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   LEU A 568 " --> pdb=" O   ASP A 616 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   ASP A 616 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLY A 570 " --> pdb=" O   ILE A 614 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   SER A 574 " --> pdb=" O   SER A 610 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   SER A 610 " --> pdb=" O   SER A 574 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223
      removed outlier: 6.052A  pdb=" N   LEU A 222 " --> pdb=" O   LEU A 238 " (cutoff:3.500A)
      removed outlier: 8.091A  pdb=" N   VAL A 237 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   THR A 201 " --> pdb=" O   VAL A 237 " (cutoff:3.500A)
      removed outlier: 7.516A  pdb=" N   CYS A 239 " --> pdb=" O   THR A 201 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   ILE A 203 " --> pdb=" O   CYS A 239 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   SER A 184 " --> pdb=" O   ASN A 204 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   GLU A 168 " --> pdb=" O   SER A 184 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   THR A 186 " --> pdb=" O   ASP A 166 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   ASP A 166 " --> pdb=" O   THR A 186 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   TYR A 188 " --> pdb=" O   PHE A 164 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   PHE A 164 " --> pdb=" O   TYR A 188 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   TYR A 190 " --> pdb=" O   TYR A 162 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   TYR A 162 " --> pdb=" O   TYR A 190 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   LEU A 163 " --> pdb=" O   VAL A 260 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 287
    Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 302
    Processing sheet with id=AA7, first strand: chain 'A' and resid 369 through 372
      removed outlier: 3.577A  pdb=" N   GLY A 372 " --> pdb=" O   PHE A 415 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   PHE A 415 " --> pdb=" O   GLY A 372 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   GLY A 414 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   ILE A 410 " --> pdb=" O   GLY A 414 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   LYS A 416 " --> pdb=" O   LYS A 408 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   LYS A 408 " --> pdb=" O   LYS A 416 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   VAL A 418 " --> pdb=" O   ILE A 406 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   LYS A 404 " --> pdb=" O   SER A 420 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   CYS A 403 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   VAL A 395 " --> pdb=" O   CYS A 403 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 705 through 706
      removed outlier: 7.048A  pdb=" N   PHE A 756 " --> pdb=" O   VAL A 748 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   GLY A 750 " --> pdb=" O   SER A 754 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   SER A 754 " --> pdb=" O   GLY A 750 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   ALA A 793 " --> pdb=" O   ILE A 547 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ASP A 549 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   PHE A 791 " --> pdb=" O   ASP A 549 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   LEU A 798 " --> pdb=" O   THR A 807 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   THR A 807 " --> pdb=" O   LEU A 798 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   MET A 800 " --> pdb=" O   LYS A 805 " (cutoff:3.500A)
      removed outlier: 7.548A  pdb=" N   LYS A 805 " --> pdb=" O   MET A 800 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 713
    Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 895
      removed outlier: 3.515A  pdb=" N   ARG A 894 " --> pdb=" O   TYR A 928 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 82
    Processing sheet with id=AB3, first strand: chain 'C' and resid 237 through 239
      removed outlier: 3.533A  pdb=" N   ILE C 238 " --> pdb=" O   SER C 222 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   SER C 222 " --> pdb=" O   ILE C 238 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 375 through 377
    Processing sheet with id=AB5, first strand: chain 'B' and resid 2 through 4
    Processing sheet with id=AB6, first strand: chain 'B' and resid 115 through 120
      removed outlier: 6.732A  pdb=" N   GLY B 115 " --> pdb=" O   LYS B  60 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   ARG B  61 " --> pdb=" O   VAL B 154 " (cutoff:3.500A)
      removed outlier: 7.756A  pdb=" N   TYR B 156 " --> pdb=" O   ARG B  61 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   CYS B  63 " --> pdb=" O   TYR B 156 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   LEU B 158 " --> pdb=" O   CYS B  63 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   CYS B  65 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   LEU B 155 " --> pdb=" O   ILE B 177 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   GLY B 179 " --> pdb=" O   LEU B 155 " (cutoff:3.500A)
      removed outlier: 5.946A  pdb=" N   CYS B 157 " --> pdb=" O   GLY B 179 " (cutoff:3.500A)

    492 hydrogen bonds defined for protein.
    1398 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      3 hydrogen bonds
      6 hydrogen bond angles
      0 basepair planarities
      1 basepair parallelities
      18 stacking parallelities
  Total time for adding SS restraints: 1.87

  Time building geometry restraints manager: 1.14 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: 4173
        1.34 -     1.45: 2377
        1.45 -     1.57: 7773
        1.57 -     1.69: 63
        1.69 -     1.81: 110
  Bond restraints: 14496
  Sorted by residual:
  bond pdb=" C3'  DT D  -6 "
       pdb=" C2'  DT D  -6 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 8.00e-03 1.56e+04 1.33e+01
  bond pdb=" C1'  DC D -13 "
       pdb=" N1   DC D -13 "
    ideal  model  delta    sigma   weight residual
    1.468  1.502 -0.034 1.40e-02 5.10e+03 5.82e+00
  bond pdb=" C1'  DC D  -8 "
       pdb=" N1   DC D  -8 "
    ideal  model  delta    sigma   weight residual
    1.468  1.500 -0.032 1.40e-02 5.10e+03 5.21e+00
  bond pdb=" C3'  DA E  -2 "
       pdb=" C2'  DA E  -2 "
    ideal  model  delta    sigma   weight residual
    1.516  1.534 -0.018 8.00e-03 1.56e+04 4.92e+00
  bond pdb=" C1'  DC D   1 "
       pdb=" N1   DC D   1 "
    ideal  model  delta    sigma   weight residual
    1.468  1.498 -0.030 1.40e-02 5.10e+03 4.46e+00
  ... (remaining 14491 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 19400
        1.95 -     3.91: 287
        3.91 -     5.86: 38
        5.86 -     7.81: 3
        7.81 -     9.77: 3
  Bond angle restraints: 19731
  Sorted by residual:
  angle pdb=" C   SER A 884 "
        pdb=" CA  SER A 884 "
        pdb=" CB  SER A 884 "
      ideal   model   delta    sigma   weight residual
     117.23  111.15    6.08 1.36e+00 5.41e-01 2.00e+01
  angle pdb=" N3   DT E   3 "
        pdb=" C4   DT E   3 "
        pdb=" O4   DT E   3 "
      ideal   model   delta    sigma   weight residual
     119.90  122.41   -2.51 6.00e-01 2.78e+00 1.74e+01
  angle pdb=" N3   DT D  -7 "
        pdb=" C4   DT D  -7 "
        pdb=" O4   DT D  -7 "
      ideal   model   delta    sigma   weight residual
     119.90  122.39   -2.49 6.00e-01 2.78e+00 1.72e+01
  angle pdb=" N3   DT E -11 "
        pdb=" C4   DT E -11 "
        pdb=" O4   DT E -11 "
      ideal   model   delta    sigma   weight residual
     119.90  122.37   -2.47 6.00e-01 2.78e+00 1.69e+01
  angle pdb=" N3   DT D -10 "
        pdb=" C4   DT D -10 "
        pdb=" O4   DT D -10 "
      ideal   model   delta    sigma   weight residual
     119.90  122.34   -2.44 6.00e-01 2.78e+00 1.66e+01
  ... (remaining 19726 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.91: 8434
       35.91 -    71.81: 220
       71.81 -   107.72: 11
      107.72 -   143.63: 1
      143.63 -   179.53: 3
  Dihedral angle restraints: 8669
    sinusoidal: 3777
      harmonic: 4892
  Sorted by residual:
  dihedral pdb=" CA  GLY A 325 "
           pdb=" C   GLY A 325 "
           pdb=" N   THR A 326 "
           pdb=" CA  THR A 326 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.47   20.53     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" C4'  DA D -11 "
           pdb=" C3'  DA D -11 "
           pdb=" O3'  DA D -11 "
           pdb=" P    DT D -10 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.53 -179.53     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DA E  -2 "
           pdb=" C3'  DA E  -2 "
           pdb=" O3'  DA E  -2 "
           pdb=" P    DA E  -1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   30.28 -170.28     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 8666 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1291
       0.030 -    0.059: 591
       0.059 -    0.089: 182
       0.089 -    0.119: 92
       0.119 -    0.148: 27
  Chirality restraints: 2183
  Sorted by residual:
  chirality pdb=" CB  ILE C  45 "
            pdb=" CA  ILE C  45 "
            pdb=" CG1 ILE C  45 "
            pdb=" CG2 ILE C  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.79   -0.15 2.00e-01 2.50e+01 5.51e-01
  chirality pdb=" CB  ILE C 245 "
            pdb=" CA  ILE C 245 "
            pdb=" CG1 ILE C 245 "
            pdb=" CG2 ILE C 245 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 5.06e-01
  chirality pdb=" P    DA E  -1 "
            pdb=" OP1  DA E  -1 "
            pdb=" OP2  DA E  -1 "
            pdb=" O5'  DA E  -1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.47   -0.14 2.00e-01 2.50e+01 4.86e-01
  ... (remaining 2180 not shown)

  Planarity restraints: 2397
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B   9 "    0.037 5.00e-02 4.00e+02   5.55e-02 4.93e+00
        pdb=" N   PRO B  10 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO B  10 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B  10 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 918 "    0.029 5.00e-02 4.00e+02   4.39e-02 3.08e+00
        pdb=" N   PRO A 919 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 919 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 919 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 149 "    0.009 2.00e-02 2.50e+03   1.74e-02 3.03e+00
        pdb=" C   VAL C 149 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   VAL C 149 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ASN C 150 "    0.010 2.00e-02 2.50e+03
  ... (remaining 2394 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 363
        2.70 -     3.25: 13749
        3.25 -     3.80: 21780
        3.80 -     4.35: 28715
        4.35 -     4.90: 47162
  Nonbonded interactions: 111769
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  40 "
            pdb=" O   LYS A  96 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" O   GLU A 339 "
            pdb=" OH  TYR A 344 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   ASP C  72 "
            pdb=" OH  TYR C  76 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   LYS A 796 "
            pdb=" OG1 THR A 808 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" OG  SER B  81 "
            pdb=" OD1 ASN B  83 "
     model   vdw
     2.253 3.040
  ... (remaining 111764 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:             4.710
  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:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.740
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  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:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14496  Z= 0.183
  Angle     :  0.565   9.769  19731  Z= 0.343
  Chirality :  0.042   0.148   2183
  Planarity :  0.004   0.056   2397
  Dihedral  : 15.988 179.534   5515
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  9.26 %
    Favored  : 90.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.21), residues: 1642
  helix:  1.12 (0.23), residues: 563
  sheet:  0.08 (0.35), residues: 259
  loop : -2.20 (0.21), residues: 820

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 255 
 TYR   0.018   0.001   TYR A 658 
 PHE   0.014   0.001   PHE A 526 
 TRP   0.013   0.001   TRP C  37 
 HIS   0.004   0.001   HIS A 897 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.18 (14496)
  covalent geometry    : angle       0.56499 /  0.34 (19731)
  hydrogen bonds       : bond        0.16178 / 10.48 (  495)
  hydrogen bonds       : angle       5.96275 /  4.08 ( 1404)

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

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

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 329
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  472 TYR cc_start: 0.7203 (t80) cc_final: 0.6966 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 329
  average time/residue: 0.1158
  time to fit residues: 53.2606
Evaluate side-chains
  192 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 98 optimal weight:    0.0000
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    0.5980
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    0.0670
   overall best weight:    0.7326

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 303 ASN
A 538 GLN
A 576 ASN
** C   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  31 ASN
B 151 HIS
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 206 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.227062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.154611 restraints weight = 17848.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3881 rms_B_bonded: 3.48
r_work: 0.3700 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3708
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3708 r_free = 0.3708    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       25 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3706 r_free = 0.3706    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (10 function evaluations)
r_final: 0.3706
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14496  Z= 0.160
  Angle     :  0.643  10.570  19731  Z= 0.341
  Chirality :  0.046   0.348   2183
  Planarity :  0.005   0.055   2397
  Dihedral  : 15.538 175.545   2172
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  9.44 %
    Favored  : 89.83 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  9.32 %
    Favored  : 89.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.21), residues: 1642
  helix:  1.30 (0.22), residues: 566
  sheet:  0.03 (0.33), residues: 273
  loop : -2.26 (0.21), residues: 803

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 744 
 TYR   0.025   0.002   TYR C  89 
 PHE   0.021   0.002   PHE A 930 
 TRP   0.015   0.002   TRP A 470 
 HIS   0.010   0.001   HIS B 181 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.16 (14496)
  covalent geometry    : angle       0.64261 /  0.34 (19731)
  hydrogen bonds       : bond        0.05355 /  3.68 (  495)
  hydrogen bonds       : angle       4.80313 /  3.33 ( 1404)

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

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

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 202
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 GLU cc_start: 0.7567 (mm-30) cc_final: 0.6859 (mt-10)
REVERT: A  472 TYR cc_start: 0.7203 (t80) cc_final: 0.6928 (t80)
REVERT: A  539 LYS cc_start: 0.7660 (ttmm) cc_final: 0.7291 (tttp)
REVERT: A  894 ARG cc_start: 0.6408 (ttp80) cc_final: 0.6115 (ttp80)
REVERT: A  895 MET cc_start: 0.6561 (ttp) cc_final: 0.5983 (ttp)
REVERT: C  129 PHE cc_start: 0.7099 (m-10) cc_final: 0.6849 (m-80)
REVERT: C  138 MET cc_start: 0.5987 (ptm) cc_final: 0.5603 (ptm)
REVERT: C  184 MET cc_start: 0.7161 (mmm) cc_final: 0.6413 (mmm)
REVERT: C  188 PHE cc_start: 0.4691 (m-10) cc_final: 0.3585 (m-80)
REVERT: C  226 ASP cc_start: 0.7577 (p0) cc_final: 0.6642 (m-30)
REVERT: B   15 TYR cc_start: 0.6221 (p90) cc_final: 0.5819 (p90)
REVERT: B  167 ARG cc_start: 0.6969 (mtt-85) cc_final: 0.6718 (mtp180)
  outliers start: 17
  outliers final: 7
  residues processed: 215
  average time/residue: 0.1347
  time to fit residues: 41.1935
Evaluate side-chains
  172 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 165
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain C residue  234 ILE
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  205 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 133 optimal weight:    9.9990
   chunk 41 optimal weight:    2.9990
   chunk 114 optimal weight:   30.0000
   chunk 104 optimal weight:    2.9990
   chunk 102 optimal weight:   10.0000
   chunk 76 optimal weight:    0.0870
   chunk 158 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   chunk 5 optimal weight:    8.9990
   chunk 93 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.8560

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 322 ASN
A 336 GLN
A 937 ASN
** C   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4657 r_free = 0.4657 target = 0.225775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.151846 restraints weight = 17848.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3878 rms_B_bonded: 3.24
r_work: 0.3670 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3680
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3680 r_free = 0.3680    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3680 r_free = 0.3680    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3680
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  14496  Z= 0.159
  Angle     :  0.616  11.899  19731  Z= 0.327
  Chirality :  0.044   0.269   2183
  Planarity :  0.005   0.056   2397
  Dihedral  : 15.522 174.197   2172
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  9.44 %
    Favored  : 89.83 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 12.02 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.21), residues: 1642
  helix:  1.28 (0.22), residues: 566
  sheet: -0.07 (0.33), residues: 271
  loop : -2.26 (0.21), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 259 
 TYR   0.020   0.001   TYR A 658 
 PHE   0.022   0.002   PHE A 930 
 TRP   0.013   0.002   TRP A 470 
 HIS   0.005   0.001   HIS A 170 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00357 /  0.16 (14496)
  covalent geometry    : angle       0.61639 /  0.33 (19731)
  hydrogen bonds       : bond        0.05003 /  3.50 (  495)
  hydrogen bonds       : angle       4.60140 /  3.19 ( 1404)

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

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

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 185
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  472 TYR cc_start: 0.7254 (t80) cc_final: 0.6936 (t80)
REVERT: A  539 LYS cc_start: 0.7623 (ttmm) cc_final: 0.7288 (tttp)
REVERT: A  895 MET cc_start: 0.6742 (ttp) cc_final: 0.6364 (ttp)
REVERT: A  923 GLU cc_start: 0.7525 (mm-30) cc_final: 0.6280 (pt0)
REVERT: C  129 PHE cc_start: 0.6995 (m-10) cc_final: 0.6720 (m-80)
REVERT: C  184 MET cc_start: 0.7204 (mmm) cc_final: 0.6623 (mmm)
REVERT: C  226 ASP cc_start: 0.7524 (p0) cc_final: 0.6557 (m-30)
REVERT: C  378 LYS cc_start: 0.8654 (tptp) cc_final: 0.8104 (tptp)
REVERT: B   15 TYR cc_start: 0.6251 (p90) cc_final: 0.5793 (p90)
  outliers start: 31
  outliers final: 17
  residues processed: 205
  average time/residue: 0.1416
  time to fit residues: 41.3299
Evaluate side-chains
  185 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 168
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  521 GLU
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  838 PHE
Chi-restraints excluded: chain A residue  891 MET
Chi-restraints excluded: chain A residue 1002 THR
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  210 VAL
Chi-restraints excluded: chain C residue  234 ILE
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 150 optimal weight:    9.9990
   chunk 106 optimal weight:    5.9990
   chunk 139 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9990
   chunk 158 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 95 optimal weight:    0.0030
   chunk 73 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    1.3796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 946 ASN
** C   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 115 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.224968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.151917 restraints weight = 18136.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3901 rms_B_bonded: 3.37
r_work: 0.3698 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3842
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3842 r_free = 0.3842    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3842 r_free = 0.3842    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3842
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  14496  Z= 0.201
  Angle     :  0.655   9.851  19731  Z= 0.347
  Chirality :  0.045   0.273   2183
  Planarity :  0.005   0.054   2397
  Dihedral  : 15.542 174.063   2172
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  9.56 %
    Favored  : 89.71 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 13.26 %
    Favored  : 84.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.13 (0.21), residues: 1642
  helix:  1.05 (0.22), residues: 562
  sheet: -0.20 (0.33), residues: 271
  loop : -2.37 (0.20), residues: 809

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 894 
 TYR   0.019   0.002   TYR A 658 
 PHE   0.026   0.002   PHE C 188 
 TRP   0.016   0.002   TRP A 470 
 HIS   0.008   0.001   HIS A 170 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00476 /  0.20 (14496)
  covalent geometry    : angle       0.65521 /  0.35 (19731)
  hydrogen bonds       : bond        0.05398 /  3.76 (  495)
  hydrogen bonds       : angle       4.66955 /  3.23 ( 1404)

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

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

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 184
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  539 LYS cc_start: 0.7738 (ttmm) cc_final: 0.7479 (tttp)
REVERT: A  742 ARG cc_start: 0.8195 (mmm160) cc_final: 0.7536 (mmm160)
REVERT: A  856 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6366 (tm-30)
REVERT: A  859 MET cc_start: 0.3269 (pmm) cc_final: 0.3025 (ppp)
REVERT: A  894 ARG cc_start: 0.7167 (ttp80) cc_final: 0.6856 (ttp80)
REVERT: A  895 MET cc_start: 0.6958 (ttp) cc_final: 0.6705 (ttp)
REVERT: C  129 PHE cc_start: 0.7061 (m-10) cc_final: 0.6726 (m-80)
REVERT: C  226 ASP cc_start: 0.7593 (p0) cc_final: 0.6671 (m-30)
REVERT: C  378 LYS cc_start: 0.8687 (tptp) cc_final: 0.8171 (tptp)
REVERT: B   15 TYR cc_start: 0.6380 (p90) cc_final: 0.5887 (p90)
  outliers start: 40
  outliers final: 28
  residues processed: 214
  average time/residue: 0.1400
  time to fit residues: 43.1561
Evaluate side-chains
  197 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 168
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  521 GLU
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  838 PHE
Chi-restraints excluded: chain A residue  856 GLU
Chi-restraints excluded: chain A residue  891 MET
Chi-restraints excluded: chain A residue  910 LEU
Chi-restraints excluded: chain A residue  918 ASN
Chi-restraints excluded: chain A residue 1002 THR
Chi-restraints excluded: chain C residue  115 ASN
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  210 VAL
Chi-restraints excluded: chain C residue  234 ILE
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 95 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 135 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 151 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 709 ASN
A 937 ASN
** C   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4679 r_free = 0.4679 target = 0.223917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.149280 restraints weight = 18136.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3879 rms_B_bonded: 3.19
r_work: 0.3700 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3844
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3844 r_free = 0.3844    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3844 r_free = 0.3844    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (7 function evaluations)
r_final: 0.3844
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.3011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14496  Z= 0.191
  Angle     :  0.660  11.828  19731  Z= 0.347
  Chirality :  0.045   0.274   2183
  Planarity :  0.005   0.093   2397
  Dihedral  : 15.536 173.975   2172
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  9.32 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 14.97 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.21), residues: 1642
  helix:  1.03 (0.22), residues: 558
  sheet: -0.35 (0.33), residues: 270
  loop : -2.43 (0.20), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 692 
 TYR   0.021   0.002   TYR B 180 
 PHE   0.022   0.002   PHE A 791 
 TRP   0.015   0.002   TRP A 470 
 HIS   0.006   0.001   HIS A 170 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00448 /  0.19 (14496)
  covalent geometry    : angle       0.65989 /  0.35 (19731)
  hydrogen bonds       : bond        0.05236 /  3.65 (  495)
  hydrogen bonds       : angle       4.61050 /  3.20 ( 1404)

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

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

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 179
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  539 LYS cc_start: 0.7523 (ttmm) cc_final: 0.7301 (ttmt)
REVERT: A  742 ARG cc_start: 0.8158 (mmm160) cc_final: 0.7933 (mmm160)
REVERT: A  856 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6361 (tm-30)
REVERT: A  859 MET cc_start: 0.3204 (pmm) cc_final: 0.2972 (ppp)
REVERT: A  895 MET cc_start: 0.6979 (ttp) cc_final: 0.6714 (ttp)
REVERT: A  922 ILE cc_start: 0.5957 (OUTLIER) cc_final: 0.5700 (mp)
REVERT: C  129 PHE cc_start: 0.7044 (m-10) cc_final: 0.6727 (m-80)
REVERT: C  210 VAL cc_start: 0.5335 (OUTLIER) cc_final: 0.5118 (p)
REVERT: C  226 ASP cc_start: 0.7576 (p0) cc_final: 0.6772 (t0)
REVERT: C  378 LYS cc_start: 0.8667 (tptp) cc_final: 0.8133 (tptp)
REVERT: B   15 TYR cc_start: 0.6402 (p90) cc_final: 0.5885 (p90)
REVERT: B   45 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7459 (mp)
REVERT: B  165 ASN cc_start: 0.8113 (t0) cc_final: 0.7705 (t0)
  outliers start: 44
  outliers final: 29
  residues processed: 213
  average time/residue: 0.1298
  time to fit residues: 40.3162
Evaluate side-chains
  203 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 170
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  521 GLU
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  838 PHE
Chi-restraints excluded: chain A residue  856 GLU
Chi-restraints excluded: chain A residue  891 MET
Chi-restraints excluded: chain A residue  910 LEU
Chi-restraints excluded: chain A residue  918 ASN
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain A residue 1002 THR
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  210 VAL
Chi-restraints excluded: chain C residue  234 ILE
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   45 ILE
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 156 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 151 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 5 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 108 optimal weight:    9.9990
   chunk 133 optimal weight:    8.9990
   chunk 132 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 130 optimal weight:    2.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 GLN
** C   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 115 ASN
B 147 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4671 r_free = 0.4671 target = 0.223067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.149367 restraints weight = 18056.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3889 rms_B_bonded: 3.19
r_work: 0.3687 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3831
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3831 r_free = 0.3831    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3831 r_free = 0.3831    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3831
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  14496  Z= 0.193
  Angle     :  0.664  11.842  19731  Z= 0.345
  Chirality :  0.045   0.275   2183
  Planarity :  0.005   0.066   2397
  Dihedral  : 15.530 173.953   2172
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  9.50 %
    Favored  : 89.77 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.89 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.21), residues: 1642
  helix:  0.99 (0.22), residues: 555
  sheet: -0.42 (0.33), residues: 270
  loop : -2.45 (0.20), residues: 817

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 894 
 TYR   0.020   0.002   TYR B 180 
 PHE   0.024   0.002   PHE A 791 
 TRP   0.015   0.002   TRP A 470 
 HIS   0.007   0.001   HIS A 170 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00456 /  0.19 (14496)
  covalent geometry    : angle       0.66368 /  0.35 (19731)
  hydrogen bonds       : bond        0.05219 /  3.65 (  495)
  hydrogen bonds       : angle       4.57412 /  3.16 ( 1404)

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

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

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 178
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 PHE cc_start: 0.7244 (t80) cc_final: 0.6873 (t80)
REVERT: A  742 ARG cc_start: 0.8165 (mmm160) cc_final: 0.7948 (mmm160)
REVERT: A  856 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6297 (tm-30)
REVERT: A  875 ASP cc_start: 0.7132 (m-30) cc_final: 0.6836 (m-30)
REVERT: A  894 ARG cc_start: 0.7410 (ttp80) cc_final: 0.7130 (ttp80)
REVERT: A  895 MET cc_start: 0.6938 (ttp) cc_final: 0.6645 (ttp)
REVERT: A  922 ILE cc_start: 0.6027 (OUTLIER) cc_final: 0.5781 (mp)
REVERT: A  972 PHE cc_start: 0.6298 (OUTLIER) cc_final: 0.6030 (m-80)
REVERT: C  129 PHE cc_start: 0.7157 (m-10) cc_final: 0.6830 (m-80)
REVERT: C  210 VAL cc_start: 0.5261 (OUTLIER) cc_final: 0.5049 (p)
REVERT: C  226 ASP cc_start: 0.7590 (p0) cc_final: 0.6767 (t0)
REVERT: C  378 LYS cc_start: 0.8677 (tptp) cc_final: 0.8147 (tptp)
REVERT: B   15 TYR cc_start: 0.6464 (p90) cc_final: 0.5837 (p90)
REVERT: B   45 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7440 (mp)
REVERT: B  165 ASN cc_start: 0.8220 (t0) cc_final: 0.7822 (t0)
  outliers start: 48
  outliers final: 34
  residues processed: 214
  average time/residue: 0.1274
  time to fit residues: 39.8841
Evaluate side-chains
  209 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 170
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  373 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  521 GLU
Chi-restraints excluded: chain A residue  543 ASN
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  604 ARG
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  838 PHE
Chi-restraints excluded: chain A residue  856 GLU
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain A residue  891 MET
Chi-restraints excluded: chain A residue  910 LEU
Chi-restraints excluded: chain A residue  918 ASN
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain A residue  972 PHE
Chi-restraints excluded: chain A residue 1002 THR
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  210 VAL
Chi-restraints excluded: chain C residue  234 ILE
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   45 ILE
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 130 optimal weight:    2.9990
   chunk 107 optimal weight:   20.0000
   chunk 157 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   chunk 35 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 937 ASN
** C   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4671 r_free = 0.4671 target = 0.223149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.148290 restraints weight = 17921.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3869 rms_B_bonded: 3.06
r_work: 0.3695 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3840
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3840 r_free = 0.3840    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3840 r_free = 0.3840    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3840
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.3365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  14496  Z= 0.173
  Angle     :  0.652  12.453  19731  Z= 0.340
  Chirality :  0.045   0.287   2183
  Planarity :  0.004   0.047   2397
  Dihedral  : 15.515 173.782   2172
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  9.56 %
    Favored  : 89.77 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 16.41 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.21), residues: 1642
  helix:  0.98 (0.22), residues: 562
  sheet: -0.43 (0.33), residues: 264
  loop : -2.47 (0.20), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 894 
 TYR   0.018   0.001   TYR A 658 
 PHE   0.023   0.002   PHE A 791 
 TRP   0.015   0.002   TRP A   8 
 HIS   0.006   0.001   HIS A 170 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00400 /  0.17 (14496)
  covalent geometry    : angle       0.65219 /  0.34 (19731)
  hydrogen bonds       : bond        0.05020 /  3.52 (  495)
  hydrogen bonds       : angle       4.52502 /  3.14 ( 1404)

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

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

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 183
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.7068 (tt0) cc_final: 0.6506 (tp30)
REVERT: A  709 ASN cc_start: 0.8340 (t0) cc_final: 0.8015 (t0)
REVERT: A  742 ARG cc_start: 0.8141 (mmm160) cc_final: 0.7890 (mmm160)
REVERT: A  751 ASP cc_start: 0.7886 (m-30) cc_final: 0.7621 (t0)
REVERT: A  856 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6280 (tm-30)
REVERT: A  859 MET cc_start: 0.4486 (ppp) cc_final: 0.2103 (mtp)
REVERT: A  875 ASP cc_start: 0.7076 (m-30) cc_final: 0.6834 (m-30)
REVERT: A  894 ARG cc_start: 0.7376 (ttp80) cc_final: 0.7088 (ttp80)
REVERT: A  895 MET cc_start: 0.6986 (ttp) cc_final: 0.6695 (ttp)
REVERT: A  922 ILE cc_start: 0.5970 (OUTLIER) cc_final: 0.5698 (mp)
REVERT: A  972 PHE cc_start: 0.6303 (OUTLIER) cc_final: 0.6058 (m-80)
REVERT: C   21 ARG cc_start: 0.6000 (mmp-170) cc_final: 0.5637 (mmp-170)
REVERT: C  129 PHE cc_start: 0.7183 (m-10) cc_final: 0.6822 (m-80)
REVERT: C  226 ASP cc_start: 0.7699 (p0) cc_final: 0.6939 (t0)
REVERT: C  378 LYS cc_start: 0.8662 (tptp) cc_final: 0.8125 (tptp)
REVERT: B   15 TYR cc_start: 0.6476 (p90) cc_final: 0.5989 (p90)
REVERT: B   45 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7477 (mp)
REVERT: B  165 ASN cc_start: 0.8075 (t0) cc_final: 0.7791 (t0)
  outliers start: 49
  outliers final: 34
  residues processed: 220
  average time/residue: 0.1233
  time to fit residues: 39.7918
Evaluate side-chains
  209 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 171
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  373 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  486 TYR
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  521 GLU
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  604 ARG
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  838 PHE
Chi-restraints excluded: chain A residue  856 GLU
Chi-restraints excluded: chain A residue  910 LEU
Chi-restraints excluded: chain A residue  918 ASN
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain A residue  972 PHE
Chi-restraints excluded: chain A residue 1002 THR
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  234 ILE
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   45 ILE
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 140 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 83 optimal weight:    0.2980
   chunk 137 optimal weight:    0.9990
   chunk 136 optimal weight:    0.4980
   chunk 10 optimal weight:    2.9990
   chunk 142 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 442 GLN
** C   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.224621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.156073 restraints weight = 18047.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3963 rms_B_bonded: 3.31
r_work: 0.3700 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3841
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3841 r_free = 0.3841    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3841 r_free = 0.3841    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3841
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.3447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14496  Z= 0.136
  Angle     :  0.623  11.455  19731  Z= 0.325
  Chirality :  0.044   0.278   2183
  Planarity :  0.004   0.048   2397
  Dihedral  : 15.488 173.558   2172
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  9.07 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.07 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.21), residues: 1642
  helix:  1.10 (0.22), residues: 556
  sheet: -0.31 (0.34), residues: 264
  loop : -2.38 (0.20), residues: 822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG C 255 
 TYR   0.019   0.001   TYR A 658 
 PHE   0.022   0.002   PHE A 930 
 TRP   0.015   0.001   TRP A   8 
 HIS   0.004   0.001   HIS C 252 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.14 (14496)
  covalent geometry    : angle       0.62280 /  0.32 (19731)
  hydrogen bonds       : bond        0.04494 /  3.17 (  495)
  hydrogen bonds       : angle       4.45341 /  3.09 ( 1404)

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

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

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 179
  time to evaluate  : 0.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.7109 (tt0) cc_final: 0.6535 (tp30)
REVERT: A  218 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7529 (m-30)
REVERT: A  267 PHE cc_start: 0.7357 (t80) cc_final: 0.7090 (t80)
REVERT: A  709 ASN cc_start: 0.8377 (t0) cc_final: 0.8058 (t0)
REVERT: A  751 ASP cc_start: 0.7821 (m-30) cc_final: 0.7610 (t0)
REVERT: A  856 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6338 (tm-30)
REVERT: A  859 MET cc_start: 0.4552 (ppp) cc_final: 0.2063 (mtp)
REVERT: A  875 ASP cc_start: 0.7133 (m-30) cc_final: 0.6883 (m-30)
REVERT: A  894 ARG cc_start: 0.7483 (ttp80) cc_final: 0.6991 (ttp80)
REVERT: A  895 MET cc_start: 0.7026 (ttp) cc_final: 0.6744 (ttp)
REVERT: A  922 ILE cc_start: 0.5983 (OUTLIER) cc_final: 0.5678 (mp)
REVERT: A  972 PHE cc_start: 0.6127 (OUTLIER) cc_final: 0.5911 (m-80)
REVERT: C   21 ARG cc_start: 0.6017 (mmp-170) cc_final: 0.5602 (mmp-170)
REVERT: C  129 PHE cc_start: 0.7184 (m-10) cc_final: 0.6924 (m-80)
REVERT: C  226 ASP cc_start: 0.7487 (p0) cc_final: 0.6831 (t0)
REVERT: C  378 LYS cc_start: 0.8680 (tptp) cc_final: 0.8153 (tptp)
REVERT: B   15 TYR cc_start: 0.6453 (p90) cc_final: 0.5905 (p90)
REVERT: B   45 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7491 (mp)
REVERT: B  165 ASN cc_start: 0.8128 (t0) cc_final: 0.7814 (t0)
  outliers start: 45
  outliers final: 33
  residues processed: 215
  average time/residue: 0.1218
  time to fit residues: 38.4142
Evaluate side-chains
  207 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 169
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  373 ASP
Chi-restraints excluded: chain A residue  486 TYR
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  521 GLU
Chi-restraints excluded: chain A residue  543 ASN
Chi-restraints excluded: chain A residue  604 ARG
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  759 ILE
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  838 PHE
Chi-restraints excluded: chain A residue  856 GLU
Chi-restraints excluded: chain A residue  910 LEU
Chi-restraints excluded: chain A residue  918 ASN
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain A residue  972 PHE
Chi-restraints excluded: chain A residue 1002 THR
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  234 ILE
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   45 ILE
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 32 optimal weight:    0.0870
   chunk 21 optimal weight:    2.9990
   chunk 160 optimal weight:    8.9990
   chunk 5 optimal weight:    0.7980
   chunk 122 optimal weight:    9.9990
   chunk 95 optimal weight:    0.2980
   chunk 100 optimal weight:    0.0470
   chunk 76 optimal weight:    2.9990
   chunk 146 optimal weight:    0.0980
   chunk 14 optimal weight:    1.9990
   chunk 162 optimal weight:    3.9990
   overall best weight:    0.2656

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 442 GLN
A 937 ASN
** C   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4699 r_free = 0.4699 target = 0.226432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.159080 restraints weight = 18095.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3996 rms_B_bonded: 3.53
r_work: 0.3750 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3888
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3888 r_free = 0.3888    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3888 r_free = 0.3888    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (10 function evaluations)
r_final: 0.3888
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.3462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  14496  Z= 0.121
  Angle     :  0.614  10.328  19731  Z= 0.321
  Chirality :  0.043   0.281   2183
  Planarity :  0.004   0.051   2397
  Dihedral  : 15.482 173.346   2172
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  9.01 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 17.14 %
    Favored  : 80.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.21), residues: 1642
  helix:  1.19 (0.23), residues: 550
  sheet: -0.25 (0.34), residues: 264
  loop : -2.31 (0.20), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG C 255 
 TYR   0.018   0.001   TYR A 658 
 PHE   0.024   0.001   PHE A 930 
 TRP   0.015   0.001   TRP A   8 
 HIS   0.004   0.001   HIS A 839 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.12 (14496)
  covalent geometry    : angle       0.61375 /  0.32 (19731)
  hydrogen bonds       : bond        0.04101 /  2.88 (  495)
  hydrogen bonds       : angle       4.36813 /  3.02 ( 1404)

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

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

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 176
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.7022 (tt0) cc_final: 0.6480 (tp30)
REVERT: A  218 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7516 (m-30)
REVERT: A  267 PHE cc_start: 0.7230 (t80) cc_final: 0.6969 (t80)
REVERT: A  357 MET cc_start: 0.1558 (ttt) cc_final: 0.1144 (tmm)
REVERT: A  709 ASN cc_start: 0.8338 (t0) cc_final: 0.8063 (t0)
REVERT: A  856 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6387 (tm-30)
REVERT: A  859 MET cc_start: 0.4354 (ppp) cc_final: 0.2280 (mtt)
REVERT: A  895 MET cc_start: 0.7045 (ttp) cc_final: 0.6625 (ttp)
REVERT: A  922 ILE cc_start: 0.5841 (OUTLIER) cc_final: 0.5520 (mp)
REVERT: C  129 PHE cc_start: 0.7200 (m-10) cc_final: 0.6933 (m-80)
REVERT: C  226 ASP cc_start: 0.7490 (p0) cc_final: 0.6805 (t0)
REVERT: C  378 LYS cc_start: 0.8644 (tptp) cc_final: 0.8105 (tptp)
REVERT: B   15 TYR cc_start: 0.6409 (p90) cc_final: 0.5764 (p90)
REVERT: B   23 MET cc_start: 0.4213 (tpp) cc_final: 0.3733 (tpp)
REVERT: B   45 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7426 (mp)
REVERT: B  165 ASN cc_start: 0.8103 (t0) cc_final: 0.7735 (t0)
  outliers start: 40
  outliers final: 27
  residues processed: 207
  average time/residue: 0.1225
  time to fit residues: 36.5688
Evaluate side-chains
  198 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 167
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  521 GLU
Chi-restraints excluded: chain A residue  543 ASN
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  759 ILE
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  838 PHE
Chi-restraints excluded: chain A residue  856 GLU
Chi-restraints excluded: chain A residue  910 LEU
Chi-restraints excluded: chain A residue  918 ASN
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain A residue 1002 THR
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  234 ILE
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain B residue   45 ILE
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 113 optimal weight:   20.0000
   chunk 12 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 109 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0270
   chunk 63 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.9640

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4677 r_free = 0.4677 target = 0.223986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.156416 restraints weight = 18122.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3964 rms_B_bonded: 3.28
r_work: 0.3705 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3839
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3839 r_free = 0.3839    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3839 r_free = 0.3839    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3839
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.3608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  14496  Z= 0.163
  Angle     :  0.661  14.975  19731  Z= 0.343
  Chirality :  0.045   0.282   2183
  Planarity :  0.004   0.045   2397
  Dihedral  : 15.494 173.528   2172
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  9.81 %
    Favored  : 89.59 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 17.79 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.21), residues: 1642
  helix:  1.03 (0.22), residues: 557
  sheet: -0.30 (0.34), residues: 264
  loop : -2.38 (0.20), residues: 821

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 742 
 TYR   0.022   0.001   TYR A 723 
 PHE   0.038   0.002   PHE C 272 
 TRP   0.012   0.001   TRP A 470 
 HIS   0.005   0.001   HIS A 170 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00379 /  0.16 (14496)
  covalent geometry    : angle       0.66091 /  0.34 (19731)
  hydrogen bonds       : bond        0.04639 /  3.26 (  495)
  hydrogen bonds       : angle       4.42230 /  3.07 ( 1404)

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

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

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3284 Ramachandran restraints generated.
    1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 168
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.7065 (tt0) cc_final: 0.6521 (tp30)
REVERT: A  218 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7538 (m-30)
REVERT: A  357 MET cc_start: 0.1648 (ttt) cc_final: 0.1285 (tmm)
REVERT: A  709 ASN cc_start: 0.8384 (t0) cc_final: 0.8072 (t0)
REVERT: A  859 MET cc_start: 0.4343 (ppp) cc_final: 0.2476 (mtt)
REVERT: A  894 ARG cc_start: 0.7519 (ttp80) cc_final: 0.7302 (ttp80)
REVERT: A  895 MET cc_start: 0.7161 (ttp) cc_final: 0.6943 (ttp)
REVERT: A  922 ILE cc_start: 0.5977 (OUTLIER) cc_final: 0.5650 (mp)
REVERT: C  129 PHE cc_start: 0.7216 (m-10) cc_final: 0.6930 (m-80)
REVERT: C  226 ASP cc_start: 0.7496 (p0) cc_final: 0.6830 (t0)
REVERT: C  378 LYS cc_start: 0.8642 (tptp) cc_final: 0.8123 (tptp)
REVERT: B   15 TYR cc_start: 0.6462 (p90) cc_final: 0.5851 (p90)
REVERT: B   23 MET cc_start: 0.4479 (tpp) cc_final: 0.3888 (tpp)
REVERT: B   45 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7461 (mp)
REVERT: B  165 ASN cc_start: 0.8112 (t0) cc_final: 0.7739 (t0)
  outliers start: 32
  outliers final: 28
  residues processed: 195
  average time/residue: 0.1151
  time to fit residues: 32.7291
Evaluate side-chains
  194 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 163
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  486 TYR
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  521 GLU
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  759 ILE
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  838 PHE
Chi-restraints excluded: chain A residue  918 ASN
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain A residue 1002 THR
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  234 ILE
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  271 THR
Chi-restraints excluded: chain B residue   45 ILE
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 154 optimal weight:    2.9990
   chunk 116 optimal weight:    7.9990
   chunk 22 optimal weight:    0.5980
   chunk 71 optimal weight:    0.3980
   chunk 58 optimal weight:    0.5980
   chunk 74 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.224855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.154426 restraints weight = 18026.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3951 rms_B_bonded: 3.19
r_work: 0.3720 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3859
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3859 r_free = 0.3859    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3859 r_free = 0.3859    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3859
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.3652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072  14496  Z= 0.141
  Angle     :  0.636  10.980  19731  Z= 0.334
  Chirality :  0.044   0.334   2183
  Planarity :  0.004   0.045   2397
  Dihedral  : 15.500 173.289   2172
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  9.01 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.93 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.13 (0.21), residues: 1642
  helix:  1.13 (0.23), residues: 550
  sheet: -0.28 (0.34), residues: 264
  loop : -2.33 (0.20), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 894 
 TYR   0.019   0.001   TYR A 723 
 PHE   0.023   0.002   PHE A 791 
 TRP   0.014   0.001   TRP A   8 
 HIS   0.003   0.001   HIS A 170 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.14 (14496)
  covalent geometry    : angle       0.63558 /  0.33 (19731)
  hydrogen bonds       : bond        0.04346 /  3.07 (  495)
  hydrogen bonds       : angle       4.40682 /  3.07 ( 1404)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4947.73 seconds
wall clock time: 85 minutes 19.27 seconds (5119.27 seconds total)