Starting phenix.real_space_refine
on Wed Mar  4 13:52:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hpa_34929/03_2026/8hpa_34929.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hpa_34929/03_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_34929/03_2026/8hpa_34929.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hpa_34929/03_2026/8hpa_34929.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hpa_34929/03_2026/8hpa_34929.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hpa_34929/03_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-5986/lib/python3.9/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: 3.17, per 1000 atoms: 0.22
  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: 1.04
  Conformation dependent library (CDL) restraints added in 662.4 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: 1.52
  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: 2.23

  Time building geometry restraints manager: 1.53 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=" O3'  DT D  -6 "
    ideal  model  delta    sigma   weight residual
    1.422  1.462 -0.040 3.00e-02 1.11e+03 1.75e+00
  bond pdb=" C   GLN C 146 "
       pdb=" N   SER C 147 "
    ideal  model  delta    sigma   weight residual
    1.331  1.356 -0.025 2.07e-02 2.33e+03 1.47e+00
  bond pdb=" N   LEU A 889 "
       pdb=" CA  LEU A 889 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.015 1.29e-02 6.01e+03 1.36e+00
  bond pdb=" C3'  DA E  -2 "
       pdb=" O3'  DA E  -2 "
    ideal  model  delta    sigma   weight residual
    1.422  1.457 -0.035 3.00e-02 1.11e+03 1.35e+00
  bond pdb=" C   SER B  43 "
       pdb=" N   PRO B  44 "
    ideal  model  delta    sigma   weight residual
    1.332  1.347 -0.015 1.32e-02 5.74e+03 1.32e+00
  ... (remaining 14491 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 19439
        1.95 -     3.91: 249
        3.91 -     5.86: 37
        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=" C   GLN C 146 "
        pdb=" N   SER C 147 "
        pdb=" CA  SER C 147 "
      ideal   model   delta    sigma   weight residual
     121.80  131.57   -9.77 2.44e+00 1.68e-01 1.60e+01
  angle pdb=" C   HIS B   8 "
        pdb=" N   ALA B   9 "
        pdb=" CA  ALA B   9 "
      ideal   model   delta    sigma   weight residual
     121.80  131.43   -9.63 2.44e+00 1.68e-01 1.56e+01
  angle pdb=" CA  SER A 884 "
        pdb=" C   SER A 884 "
        pdb=" N   SER A 885 "
      ideal   model   delta    sigma   weight residual
     119.98  117.12    2.86 8.50e-01 1.38e+00 1.13e+01
  angle pdb=" N   ILE A 966 "
        pdb=" CA  ILE A 966 "
        pdb=" C   ILE A 966 "
      ideal   model   delta    sigma   weight residual
     106.42  111.44   -5.02 1.51e+00 4.39e-01 1.10e+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: 1335
       0.030 -    0.059: 576
       0.059 -    0.089: 159
       0.089 -    0.119: 89
       0.119 -    0.148: 24
  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=" CA  GLU B 203 "
            pdb=" N   GLU B 203 "
            pdb=" C   GLU B 203 "
            pdb=" CB  GLU B 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.70e-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:             6.240
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.190
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6805
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  14496  Z= 0.114
  Angle     :  0.545   9.769  19731  Z= 0.296
  Chirality :  0.040   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
  covalent geometry    : bond        0.00232 (14496)
  covalent geometry    : angle       0.54506 (19731)
  hydrogen bonds       : bond        0.16178 (  495)
  hydrogen bonds       : angle       5.96275 ( 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  : 0.513 
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: 0.1328
  time to fit residues: 60.5415
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  : 0.476 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
A 303 ASN
A 538 GLN
A 576 ASN
A 937 ASN
** C   9 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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4664 r_free = 0.4664 target = 0.226595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.154028 restraints weight = 17860.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3891 rms_B_bonded: 3.37
r_work: 0.3687 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3696
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3696 r_free = 0.3696    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       25 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3694 r_free = 0.3694    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.3694
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14496  Z= 0.153
  Angle     :  0.615   9.736  19731  Z= 0.327
  Chirality :  0.044   0.224   2183
  Planarity :  0.005   0.052   2397
  Dihedral  : 15.539 176.887   2172
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  9.32 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  9.46 %
    Favored  : 89.30 %
  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: -0.78 (0.21), residues: 1642
  helix:  1.35 (0.22), residues: 567
  sheet:  0.04 (0.34), residues: 269
  loop : -2.20 (0.21), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 744 
 TYR   0.021   0.001   TYR A 658 
 PHE   0.019   0.002   PHE A 930 
 TRP   0.015   0.001   TRP A 470 
 HIS   0.011   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (14496)
  covalent geometry    : angle       0.61505 (19731)
  hydrogen bonds       : bond        0.05006 (  495)
  hydrogen bonds       : angle       4.66082 ( 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
  226 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 207
  time to evaluate  : 0.508 
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  168 GLU cc_start: 0.7598 (mm-30) cc_final: 0.6822 (mt-10)
REVERT: A  472 TYR cc_start: 0.7321 (t80) cc_final: 0.7016 (t80)
REVERT: A  539 LYS cc_start: 0.7626 (ttmm) cc_final: 0.7290 (tttp)
REVERT: A  895 MET cc_start: 0.6716 (ttp) cc_final: 0.6177 (ttp)
REVERT: A  923 GLU cc_start: 0.7483 (mm-30) cc_final: 0.6256 (pt0)
REVERT: C  129 PHE cc_start: 0.6811 (m-10) cc_final: 0.6464 (m-80)
REVERT: C  184 MET cc_start: 0.7222 (mmm) cc_final: 0.6536 (mmm)
REVERT: C  188 PHE cc_start: 0.4646 (m-10) cc_final: 0.3533 (m-80)
REVERT: C  226 ASP cc_start: 0.7522 (p0) cc_final: 0.6591 (m-30)
  outliers start: 19
  outliers final: 7
  residues processed: 223
  average time/residue: 0.1219
  time to fit residues: 38.4349
Evaluate side-chains
  177 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 170
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
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  177 SER
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain B residue  116 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 133 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 114 optimal weight:    0.8980
   chunk 104 optimal weight:    0.0870
   chunk 102 optimal weight:    9.9990
   chunk 76 optimal weight:    0.1980
   chunk 158 optimal weight:    5.9990
   chunk 67 optimal weight:    0.2980
   chunk 5 optimal weight:    0.2980
   chunk 93 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.3358

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

Flipped N/Q/H residues before XYZ refinement:
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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4680 r_free = 0.4680 target = 0.228482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.156530 restraints weight = 17964.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3918 rms_B_bonded: 3.49
r_work: 0.3694 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3703
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3703 r_free = 0.3703    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3703 r_free = 0.3703    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.3703
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14496  Z= 0.121
  Angle     :  0.568   9.538  19731  Z= 0.301
  Chirality :  0.042   0.154   2183
  Planarity :  0.004   0.057   2397
  Dihedral  : 15.468 176.685   2172
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  8.47 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 10.90 %
    Favored  : 87.20 %
  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: -0.70 (0.21), residues: 1642
  helix:  1.47 (0.23), residues: 561
  sheet:  0.11 (0.33), residues: 270
  loop : -2.19 (0.21), residues: 811

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 894 
 TYR   0.021   0.001   TYR A 658 
 PHE   0.021   0.001   PHE A 743 
 TRP   0.011   0.001   TRP A   8 
 HIS   0.003   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (14496)
  covalent geometry    : angle       0.56787 (19731)
  hydrogen bonds       : bond        0.04112 (  495)
  hydrogen bonds       : angle       4.41635 ( 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
  217 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 188
  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: A  443 MET cc_start: 0.7268 (mtp) cc_final: 0.6934 (mtp)
REVERT: A  539 LYS cc_start: 0.7616 (ttmm) cc_final: 0.7337 (tttp)
REVERT: A  585 GLN cc_start: 0.7422 (mm-40) cc_final: 0.7031 (mt0)
REVERT: A  602 GLU cc_start: 0.6623 (mp0) cc_final: 0.6366 (mp0)
REVERT: A  709 ASN cc_start: 0.8421 (t0) cc_final: 0.7968 (t0)
REVERT: A  895 MET cc_start: 0.6489 (ttp) cc_final: 0.6152 (ttp)
REVERT: C  129 PHE cc_start: 0.6836 (m-10) cc_final: 0.6488 (m-10)
REVERT: C  226 ASP cc_start: 0.7454 (p0) cc_final: 0.6550 (m-30)
REVERT: C  378 LYS cc_start: 0.8671 (tptp) cc_final: 0.8097 (tptp)
REVERT: B   15 TYR cc_start: 0.6220 (p90) cc_final: 0.5815 (p90)
REVERT: B   45 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7336 (mp)
REVERT: B  165 ASN cc_start: 0.8070 (t0) cc_final: 0.7636 (t0)
  outliers start: 29
  outliers final: 14
  residues processed: 208
  average time/residue: 0.1227
  time to fit residues: 36.6059
Evaluate side-chains
  181 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 166
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
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  288 SER
Chi-restraints excluded: chain A residue  512 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  918 ASN
Chi-restraints excluded: chain A residue 1002 THR
Chi-restraints excluded: chain B residue   45 ILE
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  203 GLU
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:    0.0980
   chunk 139 optimal weight:    7.9990
   chunk 11 optimal weight:    0.1980
   chunk 158 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0670
   chunk 13 optimal weight:    0.9990
   chunk 95 optimal weight:    0.0070
   chunk 73 optimal weight:    0.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.2738

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

Flipped N/Q/H residues before XYZ refinement:
A 322 ASN
A 336 GLN
A 946 ASN
** C   9 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 = 0.4743 r_free = 0.4743 target = 0.231507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.163316 restraints weight = 18287.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.4033 rms_B_bonded: 3.41
r_work: 0.3802 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3806
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3806 r_free = 0.3806    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3806 r_free = 0.3806    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.3806
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
moved from start:          0.2787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  14496  Z= 0.113
  Angle     :  0.554   9.552  19731  Z= 0.294
  Chirality :  0.041   0.171   2183
  Planarity :  0.004   0.056   2397
  Dihedral  : 15.407 177.318   2172
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  8.65 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 12.15 %
    Favored  : 85.75 %
  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: -0.66 (0.21), residues: 1642
  helix:  1.54 (0.23), residues: 561
  sheet:  0.08 (0.33), residues: 274
  loop : -2.20 (0.21), residues: 807

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 894 
 TYR   0.020   0.001   TYR A 658 
 PHE   0.021   0.001   PHE A 791 
 TRP   0.010   0.001   TRP A   8 
 HIS   0.003   0.001   HIS A 839 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (14496)
  covalent geometry    : angle       0.55368 (19731)
  hydrogen bonds       : bond        0.03743 (  495)
  hydrogen bonds       : angle       4.30549 ( 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
  216 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 184
  time to evaluate  : 0.545 
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: 0.7127 (t80) cc_final: 0.6823 (t80)
REVERT: A  585 GLN cc_start: 0.7481 (mm-40) cc_final: 0.7179 (mt0)
REVERT: A  588 LEU cc_start: 0.7034 (mt) cc_final: 0.6830 (mm)
REVERT: A  602 GLU cc_start: 0.6667 (mp0) cc_final: 0.6457 (mp0)
REVERT: A  751 ASP cc_start: 0.7597 (m-30) cc_final: 0.7310 (t0)
REVERT: A  856 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6437 (tm-30)
REVERT: C  129 PHE cc_start: 0.6852 (m-10) cc_final: 0.6523 (m-80)
REVERT: C  160 LEU cc_start: 0.4912 (OUTLIER) cc_final: 0.4538 (tt)
REVERT: C  210 VAL cc_start: 0.5359 (OUTLIER) cc_final: 0.5156 (p)
REVERT: C  226 ASP cc_start: 0.7384 (p0) cc_final: 0.6496 (m-30)
REVERT: C  378 LYS cc_start: 0.8697 (tptp) cc_final: 0.8163 (tptp)
REVERT: B   15 TYR cc_start: 0.6325 (p90) cc_final: 0.6009 (p90)
REVERT: B   45 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7469 (mp)
REVERT: B  165 ASN cc_start: 0.8029 (t0) cc_final: 0.7748 (t0)
  outliers start: 32
  outliers final: 18
  residues processed: 207
  average time/residue: 0.1317
  time to fit residues: 38.5538
Evaluate side-chains
  190 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 168
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  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  373 ASP
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  838 PHE
Chi-restraints excluded: chain A residue  856 GLU
Chi-restraints excluded: chain A residue  918 ASN
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 B residue   45 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  203 GLU
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:    4.9990
   chunk 95 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 135 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 151 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0070
   overall best weight:    1.5604

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

Flipped N/Q/H residues before XYZ refinement:
** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 937 ASN
** C   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 147 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.223036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.147844 restraints weight = 18060.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3863 rms_B_bonded: 3.15
r_work: 0.3677 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3824
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3824 r_free = 0.3824    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 = 0.3824 r_free = 0.3824    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.3824
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.3306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  14496  Z= 0.215
  Angle     :  0.674   9.412  19731  Z= 0.355
  Chirality :  0.045   0.185   2183
  Planarity :  0.005   0.062   2397
  Dihedral  : 15.473 176.771   2172
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  : 10.05 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.51 %
    Favored  : 82.99 %
  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: -1.07 (0.21), residues: 1642
  helix:  1.14 (0.22), residues: 563
  sheet: -0.09 (0.33), residues: 267
  loop : -2.41 (0.20), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 742 
 TYR   0.021   0.002   TYR A 300 
 PHE   0.026   0.002   PHE A 200 
 TRP   0.017   0.002   TRP A 470 
 HIS   0.007   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 (14496)
  covalent geometry    : angle       0.67370 (19731)
  hydrogen bonds       : bond        0.05485 (  495)
  hydrogen bonds       : angle       4.56440 ( 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
  217 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 179
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  539 LYS cc_start: 0.7608 (tttp) cc_final: 0.7336 (tttp)
REVERT: A  709 ASN cc_start: 0.8453 (t0) cc_final: 0.8071 (t0)
REVERT: A  742 ARG cc_start: 0.8154 (mmm160) cc_final: 0.7572 (mmm160)
REVERT: A  894 ARG cc_start: 0.7078 (ttp80) cc_final: 0.6871 (ttp80)
REVERT: A  922 ILE cc_start: 0.5933 (OUTLIER) cc_final: 0.5666 (mp)
REVERT: C   21 ARG cc_start: 0.6274 (mmp-170) cc_final: 0.6047 (mmm160)
REVERT: C  129 PHE cc_start: 0.7105 (m-10) cc_final: 0.6767 (m-80)
REVERT: C  160 LEU cc_start: 0.4738 (OUTLIER) cc_final: 0.4321 (tt)
REVERT: C  226 ASP cc_start: 0.7696 (p0) cc_final: 0.6927 (t0)
REVERT: C  378 LYS cc_start: 0.8675 (tptp) cc_final: 0.8149 (tptp)
REVERT: B  165 ASN cc_start: 0.8293 (t0) cc_final: 0.7976 (t0)
  outliers start: 38
  outliers final: 23
  residues processed: 207
  average time/residue: 0.1156
  time to fit residues: 35.1384
Evaluate side-chains
  187 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 162
  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   76 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  373 ASP
Chi-restraints excluded: chain A residue  521 GLU
Chi-restraints excluded: chain A residue  540 MET
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  844 LYS
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 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  258 VAL
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  205 ASP
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:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 151 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 54 optimal weight:    0.7980
   chunk 108 optimal weight:   10.0000
   chunk 133 optimal weight:    5.9990
   chunk 132 optimal weight:    6.9990
   chunk 48 optimal weight:    0.8980
   chunk 130 optimal weight:    0.1980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 937 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 = 0.4686 r_free = 0.4686 target = 0.225206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.153119 restraints weight = 17973.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3927 rms_B_bonded: 3.21
r_work: 0.3727 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3869
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3869 r_free = 0.3869    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 = 0.3869 r_free = 0.3869    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.3869
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.3435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  14496  Z= 0.139
  Angle     :  0.596   9.300  19731  Z= 0.314
  Chirality :  0.043   0.160   2183
  Planarity :  0.004   0.048   2397
  Dihedral  : 15.405 176.321   2172
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  9.01 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 15.89 %
    Favored  : 81.88 %
  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: -0.97 (0.21), residues: 1642
  helix:  1.30 (0.23), residues: 559
  sheet: -0.14 (0.33), residues: 269
  loop : -2.35 (0.20), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 255 
 TYR   0.019   0.001   TYR A 658 
 PHE   0.021   0.001   PHE A 791 
 TRP   0.013   0.001   TRP A   8 
 HIS   0.004   0.001   HIS A 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (14496)
  covalent geometry    : angle       0.59649 (19731)
  hydrogen bonds       : bond        0.04389 (  495)
  hydrogen bonds       : angle       4.39494 ( 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
  206 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 172
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 ILE cc_start: 0.6740 (OUTLIER) cc_final: 0.6388 (mt)
REVERT: A  539 LYS cc_start: 0.7437 (tttp) cc_final: 0.7207 (tttp)
REVERT: A  709 ASN cc_start: 0.8524 (t0) cc_final: 0.7925 (t0)
REVERT: A  742 ARG cc_start: 0.8121 (mmm160) cc_final: 0.7593 (mmm160)
REVERT: A  875 ASP cc_start: 0.7200 (m-30) cc_final: 0.6977 (m-30)
REVERT: A  894 ARG cc_start: 0.7093 (ttp80) cc_final: 0.6886 (ttp80)
REVERT: C  129 PHE cc_start: 0.7088 (m-10) cc_final: 0.6655 (m-10)
REVERT: C  160 LEU cc_start: 0.4781 (OUTLIER) cc_final: 0.4365 (tt)
REVERT: C  226 ASP cc_start: 0.7552 (p0) cc_final: 0.6864 (t0)
REVERT: C  378 LYS cc_start: 0.8657 (tptp) cc_final: 0.8116 (tptp)
REVERT: B   15 TYR cc_start: 0.6384 (p90) cc_final: 0.5977 (p90)
REVERT: B   45 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7395 (mp)
REVERT: B  165 ASN cc_start: 0.8225 (t0) cc_final: 0.7884 (t0)
  outliers start: 34
  outliers final: 23
  residues processed: 200
  average time/residue: 0.1190
  time to fit residues: 34.6188
Evaluate side-chains
  189 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 163
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  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  448 ASN
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  540 MET
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  838 PHE
Chi-restraints excluded: chain A residue  918 ASN
Chi-restraints excluded: chain A residue  933 ILE
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  208 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 130 optimal weight:    3.9990
   chunk 107 optimal weight:   10.0000
   chunk 157 optimal weight:    5.9990
   chunk 51 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0060
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.9198

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

Flipped N/Q/H residues before XYZ refinement:
** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 170 HIS
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 = 0.4677 r_free = 0.4677 target = 0.224140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.160224 restraints weight = 17894.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.4006 rms_B_bonded: 3.48
r_work: 0.3695 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3832
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3832 r_free = 0.3832    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 = 0.3832 r_free = 0.3832    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.3832
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.3651

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= 0.154
  Angle     :  0.610   9.342  19731  Z= 0.321
  Chirality :  0.043   0.194   2183
  Planarity :  0.004   0.047   2397
  Dihedral  : 15.370 175.966   2172
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  9.44 %
    Favored  : 89.83 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 16.09 %
    Favored  : 81.62 %
  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: -1.08 (0.21), residues: 1642
  helix:  1.15 (0.22), residues: 563
  sheet: -0.16 (0.33), residues: 265
  loop : -2.39 (0.20), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 255 
 TYR   0.018   0.001   TYR A 723 
 PHE   0.019   0.002   PHE C 272 
 TRP   0.013   0.001   TRP A 470 
 HIS   0.005   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (14496)
  covalent geometry    : angle       0.60952 (19731)
  hydrogen bonds       : bond        0.04625 (  495)
  hydrogen bonds       : angle       4.43088 ( 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
  207 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 172
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 ILE cc_start: 0.6712 (OUTLIER) cc_final: 0.6391 (mt)
REVERT: A  357 MET cc_start: 0.1745 (ttt) cc_final: 0.1541 (tmm)
REVERT: A  709 ASN cc_start: 0.8538 (t0) cc_final: 0.7987 (t0)
REVERT: A  875 ASP cc_start: 0.7226 (m-30) cc_final: 0.7002 (m-30)
REVERT: A  922 ILE cc_start: 0.5943 (OUTLIER) cc_final: 0.5642 (mp)
REVERT: C  129 PHE cc_start: 0.7086 (m-10) cc_final: 0.6762 (m-10)
REVERT: C  160 LEU cc_start: 0.4802 (OUTLIER) cc_final: 0.4377 (tt)
REVERT: C  226 ASP cc_start: 0.7630 (p0) cc_final: 0.6939 (t0)
REVERT: C  378 LYS cc_start: 0.8683 (tptp) cc_final: 0.8153 (tptp)
REVERT: B   15 TYR cc_start: 0.6451 (p90) cc_final: 0.6038 (p90)
REVERT: B  126 LYS cc_start: 0.7947 (mmmt) cc_final: 0.7732 (mmtp)
REVERT: B  165 ASN cc_start: 0.8250 (t0) cc_final: 0.7923 (t0)
  outliers start: 35
  outliers final: 23
  residues processed: 201
  average time/residue: 0.1158
  time to fit residues: 34.2107
Evaluate side-chains
  189 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 163
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  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  391 THR
Chi-restraints excluded: chain A residue  448 ASN
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  545 VAL
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  918 ASN
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  933 ILE
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  208 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 140 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 83 optimal weight:    1.9990
   chunk 137 optimal weight:    0.8980
   chunk 136 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 142 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4679 r_free = 0.4679 target = 0.224472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.159073 restraints weight = 18041.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3995 rms_B_bonded: 3.48
r_work: 0.3703 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3703
-------------------------------------------------------------------------------
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 |
|-----------------------------------------------------------------------------|
r_final: 0.3840
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7347
moved from start:          0.3755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  14496  Z= 0.144
  Angle     :  0.615   9.393  19731  Z= 0.321
  Chirality :  0.043   0.187   2183
  Planarity :  0.004   0.047   2397
  Dihedral  : 15.359 175.712   2172
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  9.62 %
    Favored  : 89.71 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.55 %
    Favored  : 81.22 %
  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:  1.17 (0.22), residues: 563
  sheet: -0.25 (0.33), residues: 266
  loop : -2.35 (0.20), residues: 813

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 742 
 TYR   0.018   0.001   TYR A 658 
 PHE   0.020   0.002   PHE A 930 
 TRP   0.021   0.001   TRP C  37 
 HIS   0.003   0.001   HIS B   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (14496)
  covalent geometry    : angle       0.61526 (19731)
  hydrogen bonds       : bond        0.04362 (  495)
  hydrogen bonds       : angle       4.39774 ( 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
  199 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 165
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 ILE cc_start: 0.6699 (OUTLIER) cc_final: 0.6417 (mt)
REVERT: A  218 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7574 (m-30)
REVERT: A  709 ASN cc_start: 0.8547 (t0) cc_final: 0.8016 (t0)
REVERT: A  859 MET cc_start: 0.3122 (pmm) cc_final: -0.0745 (mpp)
REVERT: A  875 ASP cc_start: 0.7214 (m-30) cc_final: 0.6995 (m-30)
REVERT: A  895 MET cc_start: 0.7274 (ptm) cc_final: 0.7026 (ttp)
REVERT: A  922 ILE cc_start: 0.5897 (OUTLIER) cc_final: 0.5612 (mp)
REVERT: C   98 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.6106 (mm)
REVERT: C  129 PHE cc_start: 0.7169 (m-10) cc_final: 0.6868 (m-10)
REVERT: C  160 LEU cc_start: 0.4848 (OUTLIER) cc_final: 0.4442 (tt)
REVERT: C  226 ASP cc_start: 0.7558 (p0) cc_final: 0.6880 (t0)
REVERT: C  378 LYS cc_start: 0.8693 (tptp) cc_final: 0.8154 (tptp)
REVERT: B   15 TYR cc_start: 0.6462 (p90) cc_final: 0.6035 (p90)
REVERT: B  126 LYS cc_start: 0.7950 (mmmt) cc_final: 0.7699 (mmtp)
REVERT: B  165 ASN cc_start: 0.8222 (t0) cc_final: 0.7897 (t0)
  outliers start: 34
  outliers final: 25
  residues processed: 194
  average time/residue: 0.1184
  time to fit residues: 33.5168
Evaluate side-chains
  190 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 160
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  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  373 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  448 ASN
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  545 VAL
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  918 ASN
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  162 ILE
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  208 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0030
   chunk 160 optimal weight:    8.9990
   chunk 5 optimal weight:    3.9990
   chunk 122 optimal weight:   10.0000
   chunk 95 optimal weight:    0.9980
   chunk 100 optimal weight:    9.9990
   chunk 76 optimal weight:    1.9990
   chunk 146 optimal weight:    0.0770
   chunk 14 optimal weight:    0.5980
   chunk 162 optimal weight:    0.9980
   overall best weight:    0.5348

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4691 r_free = 0.4691 target = 0.225802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.154153 restraints weight = 18050.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 3.23
r_work: 0.3731 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3874
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3874 r_free = 0.3874    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3874 r_free = 0.3874    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.3874
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.3823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  14496  Z= 0.128
  Angle     :  0.609  11.712  19731  Z= 0.317
  Chirality :  0.042   0.179   2183
  Planarity :  0.004   0.046   2397
  Dihedral  : 15.313 175.486   2172
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  9.20 %
    Favored  : 90.19 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 16.81 %
    Favored  : 81.02 %
  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: -0.98 (0.21), residues: 1642
  helix:  1.33 (0.23), residues: 555
  sheet: -0.28 (0.33), residues: 274
  loop : -2.33 (0.20), residues: 813

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 742 
 TYR   0.018   0.001   TYR A 658 
 PHE   0.023   0.001   PHE A 930 
 TRP   0.023   0.002   TRP B 212 
 HIS   0.003   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (14496)
  covalent geometry    : angle       0.60927 (19731)
  hydrogen bonds       : bond        0.04069 (  495)
  hydrogen bonds       : angle       4.34189 ( 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
  195 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 162
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6507 (mt)
REVERT: A  218 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7548 (m-30)
REVERT: A  859 MET cc_start: 0.3129 (pmm) cc_final: -0.0617 (mpp)
REVERT: A  875 ASP cc_start: 0.7219 (m-30) cc_final: 0.6999 (m-30)
REVERT: A  895 MET cc_start: 0.7113 (ptm) cc_final: 0.6871 (ttp)
REVERT: A  922 ILE cc_start: 0.5761 (OUTLIER) cc_final: 0.5470 (mp)
REVERT: C   98 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6096 (mm)
REVERT: C  129 PHE cc_start: 0.7242 (m-10) cc_final: 0.6920 (m-10)
REVERT: C  160 LEU cc_start: 0.4789 (OUTLIER) cc_final: 0.4391 (tt)
REVERT: C  226 ASP cc_start: 0.7537 (p0) cc_final: 0.6873 (t0)
REVERT: C  333 GLU cc_start: 0.8538 (tp30) cc_final: 0.8334 (tt0)
REVERT: C  378 LYS cc_start: 0.8673 (tptp) cc_final: 0.8130 (tptp)
REVERT: B   15 TYR cc_start: 0.6456 (p90) cc_final: 0.6007 (p90)
REVERT: B   39 ARG cc_start: 0.4749 (ptt180) cc_final: 0.4514 (ptt180)
REVERT: B  165 ASN cc_start: 0.8192 (t0) cc_final: 0.7841 (t0)
REVERT: B  212 TRP cc_start: 0.7000 (m100) cc_final: 0.6698 (m100)
  outliers start: 33
  outliers final: 24
  residues processed: 189
  average time/residue: 0.1150
  time to fit residues: 31.7516
Evaluate side-chains
  180 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 151
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  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  373 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  448 ASN
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  545 VAL
Chi-restraints excluded: chain A residue  718 LEU
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 C residue   98 LEU
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  162 ILE
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  116 VAL
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:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 86 optimal weight:    6.9990
   chunk 73 optimal weight:    0.0980
   chunk 79 optimal weight:    4.9990
   chunk 109 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4673 r_free = 0.4673 target = 0.223610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.158487 restraints weight = 18145.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3982 rms_B_bonded: 3.40
r_work: 0.3688 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3827
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3827 r_free = 0.3827    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 = 0.3827 r_free = 0.3827    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.3827
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.4007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  14496  Z= 0.163
  Angle     :  0.639   9.999  19731  Z= 0.334
  Chirality :  0.043   0.172   2183
  Planarity :  0.004   0.046   2397
  Dihedral  : 15.329 175.670   2172
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  9.62 %
    Favored  : 89.71 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 16.87 %
    Favored  : 81.02 %
  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: -1.12 (0.21), residues: 1642
  helix:  1.17 (0.22), residues: 556
  sheet: -0.28 (0.33), residues: 270
  loop : -2.40 (0.20), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 742 
 TYR   0.018   0.001   TYR A 658 
 PHE   0.022   0.002   PHE A 791 
 TRP   0.029   0.002   TRP B 212 
 HIS   0.004   0.001   HIS B   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (14496)
  covalent geometry    : angle       0.63915 (19731)
  hydrogen bonds       : bond        0.04646 (  495)
  hydrogen bonds       : angle       4.45891 ( 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
  197 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 165
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 ILE cc_start: 0.6751 (OUTLIER) cc_final: 0.6444 (mt)
REVERT: A  218 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7636 (m-30)
REVERT: A  859 MET cc_start: 0.2914 (pmm) cc_final: -0.0255 (mpp)
REVERT: A  875 ASP cc_start: 0.7238 (m-30) cc_final: 0.7012 (m-30)
REVERT: A  895 MET cc_start: 0.7330 (ptm) cc_final: 0.7069 (ttp)
REVERT: A  922 ILE cc_start: 0.5944 (OUTLIER) cc_final: 0.5685 (mp)
REVERT: C   98 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.6147 (mm)
REVERT: C  129 PHE cc_start: 0.7322 (m-10) cc_final: 0.7045 (m-10)
REVERT: C  160 LEU cc_start: 0.4820 (OUTLIER) cc_final: 0.4427 (tt)
REVERT: C  226 ASP cc_start: 0.7584 (p0) cc_final: 0.6949 (t0)
REVERT: C  333 GLU cc_start: 0.8518 (tp30) cc_final: 0.8317 (tt0)
REVERT: C  378 LYS cc_start: 0.8687 (tptp) cc_final: 0.8161 (tptp)
REVERT: B   15 TYR cc_start: 0.6533 (p90) cc_final: 0.6042 (p90)
REVERT: B  165 ASN cc_start: 0.8220 (t0) cc_final: 0.7923 (t0)
REVERT: B  212 TRP cc_start: 0.6953 (m100) cc_final: 0.6626 (m100)
  outliers start: 32
  outliers final: 27
  residues processed: 192
  average time/residue: 0.1172
  time to fit residues: 32.6276
Evaluate side-chains
  189 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 157
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  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  373 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  448 ASN
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  545 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  918 ASN
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  162 ILE
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  208 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 154 optimal weight:    0.0060
   chunk 116 optimal weight:    0.0470
   chunk 22 optimal weight:    0.9980
   chunk 71 optimal weight:    0.6980
   chunk 58 optimal weight:    0.8980
   chunk 74 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.4894

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4694 r_free = 0.4694 target = 0.226134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.157696 restraints weight = 18112.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3984 rms_B_bonded: 3.16
r_work: 0.3743 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3882
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3882 r_free = 0.3882    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3882 r_free = 0.3882    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.3882
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.4037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  14496  Z= 0.127
  Angle     :  0.613   9.874  19731  Z= 0.320
  Chirality :  0.042   0.177   2183
  Planarity :  0.004   0.046   2397
  Dihedral  : 15.263 175.111   2172
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  9.50 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.74 %
    Favored  : 80.76 %
  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: -0.99 (0.21), residues: 1642
  helix:  1.28 (0.22), residues: 555
  sheet: -0.14 (0.34), residues: 266
  loop : -2.33 (0.20), residues: 821

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 617 
 TYR   0.023   0.001   TYR A 668 
 PHE   0.021   0.001   PHE A 930 
 TRP   0.026   0.002   TRP B 212 
 HIS   0.003   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (14496)
  covalent geometry    : angle       0.61252 (19731)
  hydrogen bonds       : bond        0.03965 (  495)
  hydrogen bonds       : angle       4.36077 ( 1404)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4733.54 seconds
wall clock time: 81 minutes 25.68 seconds (4885.68 seconds total)