Starting phenix.real_space_refine
on Thu Jun 12 16:05:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hpa_34929/06_2025/8hpa_34929.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hpa_34929/06_2025/8hpa_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_34929/06_2025/8hpa_34929.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hpa_34929/06_2025/8hpa_34929.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hpa_34929/06_2025/8hpa_34929.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hpa_34929/06_2025/8hpa_34929.cif"
  }
  resolution = 3.01
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.44, per 1000 atoms: 0.67
  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: 3.26
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  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: 4.86
  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: 4.87

  Time building geometry restraints manager: 3.94 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:             4.330
  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:          0.550
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     38.170
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.490
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.013   0.001   TRP C  37 
 HIS   0.004   0.001   HIS A 897 
 PHE   0.014   0.001   PHE A 526 
 TYR   0.018   0.001   TYR A 658 
 ARG   0.005   0.000   ARG C 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16178 (  495)
  hydrogen bonds       : angle       5.96275 ( 1404)
  covalent geometry    : bond        0.00232 (14496)
  covalent geometry    : angle       0.54506 (19731)

*********************** 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  : 1.510 
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: 0.6965 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 329
  average time/residue: 0.3347
  time to fit residues: 152.9138
Evaluate side-chains
  193 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 139 optimal weight:    5.9990
   chunk 125 optimal weight:   10.0000
   chunk 69 optimal weight:    2.9990
   chunk 42 optimal weight:   20.0000
   chunk 84 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 129 optimal weight:    4.9990
   chunk 50 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 149 optimal weight:    0.0670
   overall best weight:    1.3524

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

Flipped N/Q/H residues before XYZ refinement:
A 303 ASN
A 322 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**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.223083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.148949 restraints weight = 17785.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3818 rms_B_bonded: 3.45
r_work: 0.3633 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3642
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3642 r_free = 0.3642    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       25 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3640 r_free = 0.3640    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.3640
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  14496  Z= 0.205
  Angle     :  0.666  10.079  19731  Z= 0.353
  Chirality :  0.046   0.213   2183
  Planarity :  0.005   0.050   2397
  Dihedral  : 15.596 176.518   2172
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  9.74 %
    Favored  : 89.52 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 10.44 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.21), residues: 1642
  helix:  1.17 (0.22), residues: 564
  sheet:  0.02 (0.35), residues: 260
  loop : -2.31 (0.20), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 470 
 HIS   0.011   0.002   HIS B 181 
 PHE   0.023   0.002   PHE A 200 
 TYR   0.020   0.002   TYR A 658 
 ARG   0.005   0.001   ARG A 744 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05674 (  495)
  hydrogen bonds       : angle       4.74564 ( 1404)
  covalent geometry    : bond        0.00487 (14496)
  covalent geometry    : angle       0.66551 (19731)

*********************** 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
  222 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 201
  time to evaluate  : 1.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  443 MET cc_start: 0.7240 (mtp) cc_final: 0.6926 (mtp)
REVERT: A  539 LYS cc_start: 0.7649 (ttmm) cc_final: 0.7288 (tttp)
REVERT: A  742 ARG cc_start: 0.8207 (mmm160) cc_final: 0.7993 (mmm160)
REVERT: A  790 GLU cc_start: 0.7346 (pt0) cc_final: 0.7146 (pt0)
REVERT: A  875 ASP cc_start: 0.7065 (m-30) cc_final: 0.6820 (m-30)
REVERT: A  894 ARG cc_start: 0.6569 (ttp80) cc_final: 0.6366 (ttp80)
REVERT: A  895 MET cc_start: 0.6974 (ttp) cc_final: 0.6357 (ttp)
REVERT: C  129 PHE cc_start: 0.6811 (m-10) cc_final: 0.6460 (m-80)
REVERT: C  184 MET cc_start: 0.7220 (mmm) cc_final: 0.6543 (mmm)
REVERT: C  188 PHE cc_start: 0.4623 (m-80) cc_final: 0.3456 (m-80)
REVERT: C  226 ASP cc_start: 0.7618 (p0) cc_final: 0.6749 (m-30)
  outliers start: 21
  outliers final: 12
  residues processed: 218
  average time/residue: 0.2954
  time to fit residues: 91.0203
Evaluate side-chains
  179 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 167
  time to evaluate  : 1.511 
-------------------------------------------------------------------------------
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  130 GLN
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 A residue  808 THR
Chi-restraints excluded: chain C residue  234 ILE
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  143 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 53 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0670
   chunk 36 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 4 optimal weight:    0.3980
   chunk 29 optimal weight:    0.9980
   chunk 101 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 145 optimal weight:    0.8980
   overall best weight:    0.6318

-------------------------------------------------------------------------------
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**
** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 147 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4707 r_free = 0.4707 target = 0.227242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.157227 restraints weight = 18066.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3974 rms_B_bonded: 3.38
r_work: 0.3747 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3756
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3756 r_free = 0.3756    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3755 r_free = 0.3755    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.3755
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.2711

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= 0.138
  Angle     :  0.595  10.894  19731  Z= 0.313
  Chirality :  0.043   0.215   2183
  Planarity :  0.004   0.056   2397
  Dihedral  : 15.503 176.161   2172
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  8.89 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 12.61 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.21), residues: 1642
  helix:  1.35 (0.23), residues: 559
  sheet:  0.09 (0.34), residues: 266
  loop : -2.31 (0.20), residues: 817

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A   8 
 HIS   0.003   0.001   HIS A 170 
 PHE   0.020   0.002   PHE A 930 
 TYR   0.021   0.001   TYR A 658 
 ARG   0.005   0.000   ARG C 423 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04479 (  495)
  hydrogen bonds       : angle       4.43637 ( 1404)
  covalent geometry    : bond        0.00309 (14496)
  covalent geometry    : angle       0.59460 (19731)

*********************** 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: 32
    poor density    : 185
  time to evaluate  : 1.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  443 MET cc_start: 0.7379 (mtp) cc_final: 0.7043 (mtp)
REVERT: A  709 ASN cc_start: 0.8438 (t0) cc_final: 0.8083 (t0)
REVERT: A  895 MET cc_start: 0.7138 (ttp) cc_final: 0.6683 (ttp)
REVERT: C  129 PHE cc_start: 0.6918 (m-10) cc_final: 0.6385 (m-80)
REVERT: C  226 ASP cc_start: 0.7535 (p0) cc_final: 0.6793 (t0)
REVERT: C  378 LYS cc_start: 0.8693 (tptp) cc_final: 0.8174 (tptp)
REVERT: C  406 ASN cc_start: 0.7443 (m-40) cc_final: 0.6546 (t0)
REVERT: B  165 ASN cc_start: 0.8085 (t0) cc_final: 0.7711 (t0)
  outliers start: 32
  outliers final: 16
  residues processed: 206
  average time/residue: 0.3755
  time to fit residues: 112.5863
Evaluate side-chains
  180 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 164
  time to evaluate  : 2.350 
-------------------------------------------------------------------------------
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  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  891 MET
Chi-restraints excluded: chain A residue  918 ASN
Chi-restraints excluded: chain A residue 1002 THR
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  234 ILE
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  143 LEU
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 154 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 136 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 108 optimal weight:   10.0000
   chunk 62 optimal weight:    0.9990
   chunk 58 optimal weight:    0.1980
   chunk 72 optimal weight:    0.0870
   overall best weight:    0.5960

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
** C   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4705 r_free = 0.4705 target = 0.226979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.157230 restraints weight = 18010.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 3.26
r_work: 0.3743 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3748
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3748 r_free = 0.3748    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3748 r_free = 0.3748    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.3748
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14496  Z= 0.132
  Angle     :  0.593  10.115  19731  Z= 0.309
  Chirality :  0.042   0.263   2183
  Planarity :  0.004   0.054   2397
  Dihedral  : 15.449 176.196   2172
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  8.59 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.99 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.21), residues: 1642
  helix:  1.34 (0.23), residues: 560
  sheet: -0.01 (0.33), residues: 271
  loop : -2.29 (0.20), residues: 811

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A   8 
 HIS   0.004   0.001   HIS A 170 
 PHE   0.025   0.002   PHE A 791 
 TYR   0.019   0.001   TYR A 658 
 ARG   0.005   0.000   ARG A 894 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04280 (  495)
  hydrogen bonds       : angle       4.38330 ( 1404)
  covalent geometry    : bond        0.00296 (14496)
  covalent geometry    : angle       0.59313 (19731)

*********************** 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
  222 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 185
  time to evaluate  : 1.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 PHE cc_start: 0.7245 (t80) cc_final: 0.6962 (t80)
REVERT: A  357 MET cc_start: 0.1475 (ttt) cc_final: 0.1268 (tmm)
REVERT: A  709 ASN cc_start: 0.8436 (t0) cc_final: 0.7797 (t0)
REVERT: A  842 MET cc_start: 0.7386 (ttm) cc_final: 0.7143 (ttt)
REVERT: A  856 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6327 (tm-30)
REVERT: A  895 MET cc_start: 0.6990 (ttp) cc_final: 0.6590 (ttp)
REVERT: A  922 ILE cc_start: 0.5937 (OUTLIER) cc_final: 0.5655 (mp)
REVERT: C  129 PHE cc_start: 0.6918 (m-10) cc_final: 0.6532 (m-80)
REVERT: C  226 ASP cc_start: 0.7515 (p0) cc_final: 0.6716 (m-30)
REVERT: C  378 LYS cc_start: 0.8704 (tptp) cc_final: 0.8174 (tptp)
REVERT: C  406 ASN cc_start: 0.7476 (m-40) cc_final: 0.6612 (t0)
REVERT: B   15 TYR cc_start: 0.6264 (p90) cc_final: 0.5910 (p90)
REVERT: B   45 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7545 (mp)
REVERT: B  165 ASN cc_start: 0.8079 (t0) cc_final: 0.7795 (t0)
  outliers start: 37
  outliers final: 22
  residues processed: 210
  average time/residue: 0.2746
  time to fit residues: 83.7038
Evaluate side-chains
  191 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 166
  time to evaluate  : 1.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  373 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  521 GLU
Chi-restraints excluded: chain A residue  543 ASN
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  856 GLU
Chi-restraints excluded: chain A residue  918 ASN
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain A residue 1002 THR
Chi-restraints excluded: chain C residue  130 VAL
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 B residue   45 ILE
Chi-restraints excluded: chain B residue  143 LEU
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 7 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 130 optimal weight:    3.9990
   chunk 115 optimal weight:    6.9990
   chunk 103 optimal weight:    6.9990
   chunk 133 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 86 optimal weight:    8.9990
   chunk 131 optimal weight:    0.3980
   chunk 55 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 170 HIS
A 336 GLN
A 937 ASN
** C   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.222891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.149228 restraints weight = 18100.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 3.25
r_work: 0.3679 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3823
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3823 r_free = 0.3823    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 = 0.3823 r_free = 0.3823    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.3823
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.3423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  14496  Z= 0.188
  Angle     :  0.654  12.434  19731  Z= 0.341
  Chirality :  0.045   0.277   2183
  Planarity :  0.005   0.051   2397
  Dihedral  : 15.458 176.409   2172
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  9.32 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 15.43 %
    Favored  : 81.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.21), residues: 1642
  helix:  1.11 (0.22), residues: 567
  sheet: -0.10 (0.33), residues: 267
  loop : -2.44 (0.20), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 470 
 HIS   0.007   0.001   HIS A 170 
 PHE   0.023   0.002   PHE A 791 
 TYR   0.018   0.002   TYR A 658 
 ARG   0.005   0.000   ARG A 742 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05116 (  495)
  hydrogen bonds       : angle       4.51364 ( 1404)
  covalent geometry    : bond        0.00450 (14496)
  covalent geometry    : angle       0.65448 (19731)

*********************** 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
  219 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 177
  time to evaluate  : 1.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 GLN cc_start: 0.6846 (tp40) cc_final: 0.6290 (tp-100)
REVERT: A  218 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7275 (m-30)
REVERT: A  709 ASN cc_start: 0.8493 (t0) cc_final: 0.7926 (t0)
REVERT: A  742 ARG cc_start: 0.8162 (mmm160) cc_final: 0.7656 (mmm160)
REVERT: A  842 MET cc_start: 0.7487 (ttm) cc_final: 0.7097 (ttt)
REVERT: A  894 ARG cc_start: 0.7480 (ttp80) cc_final: 0.7183 (ttp80)
REVERT: A  895 MET cc_start: 0.7137 (ttp) cc_final: 0.6607 (ttp)
REVERT: A  922 ILE cc_start: 0.5983 (OUTLIER) cc_final: 0.5738 (mp)
REVERT: C  129 PHE cc_start: 0.6959 (m-10) cc_final: 0.6558 (m-10)
REVERT: C  226 ASP cc_start: 0.7718 (p0) cc_final: 0.6998 (t0)
REVERT: C  378 LYS cc_start: 0.8691 (tptp) cc_final: 0.8156 (tptp)
REVERT: B   15 TYR cc_start: 0.6449 (p90) cc_final: 0.6003 (p90)
REVERT: B   45 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7446 (mp)
REVERT: B  126 LYS cc_start: 0.7959 (mmmt) cc_final: 0.7494 (mmtm)
REVERT: B  165 ASN cc_start: 0.8258 (t0) cc_final: 0.7970 (t0)
  outliers start: 42
  outliers final: 25
  residues processed: 208
  average time/residue: 0.2797
  time to fit residues: 83.7434
Evaluate side-chains
  195 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 167
  time to evaluate  : 1.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  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  486 TYR
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  521 GLU
Chi-restraints excluded: chain A residue  543 ASN
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  918 ASN
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain A residue 1002 THR
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  234 ILE
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain B residue   45 ILE
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 121 optimal weight:    0.0570
   chunk 87 optimal weight:    7.9990
   chunk 123 optimal weight:    6.9990
   chunk 14 optimal weight:    0.6980
   chunk 91 optimal weight:    3.9990
   chunk 37 optimal weight:    8.9990
   chunk 62 optimal weight:    0.5980
   chunk 142 optimal weight:    0.0970
   chunk 109 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.4696

-------------------------------------------------------------------------------
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 336 GLN
A 937 ASN
A 963 ASN
** C   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 115 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.226464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.161709 restraints weight = 18210.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.4024 rms_B_bonded: 3.60
r_work: 0.3715 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3854
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3854 r_free = 0.3854    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 = 0.3854 r_free = 0.3854    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.3854
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.3505

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= 0.125
  Angle     :  0.593  11.110  19731  Z= 0.310
  Chirality :  0.042   0.264   2183
  Planarity :  0.004   0.049   2397
  Dihedral  : 15.386 175.914   2172
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  9.07 %
    Favored  : 90.19 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 17.20 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.21), residues: 1642
  helix:  1.31 (0.23), residues: 561
  sheet: -0.25 (0.33), residues: 272
  loop : -2.33 (0.21), residues: 809

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A   8 
 HIS   0.004   0.001   HIS A 839 
 PHE   0.021   0.001   PHE A 930 
 TYR   0.019   0.001   TYR A 658 
 ARG   0.004   0.000   ARG A 742 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04021 (  495)
  hydrogen bonds       : angle       4.33778 ( 1404)
  covalent geometry    : bond        0.00278 (14496)
  covalent geometry    : angle       0.59312 (19731)

*********************** 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
  216 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 179
  time to evaluate  : 1.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7541 (m-30)
REVERT: A  267 PHE cc_start: 0.7320 (t80) cc_final: 0.7051 (t80)
REVERT: A  357 MET cc_start: 0.1734 (ttt) cc_final: 0.1528 (tmm)
REVERT: A  709 ASN cc_start: 0.8516 (t0) cc_final: 0.7965 (t0)
REVERT: A  742 ARG cc_start: 0.8155 (mmm160) cc_final: 0.7944 (mmm160)
REVERT: A  894 ARG cc_start: 0.7463 (ttp80) cc_final: 0.7104 (ttp80)
REVERT: A  895 MET cc_start: 0.7089 (ttp) cc_final: 0.6586 (ttp)
REVERT: A  922 ILE cc_start: 0.5919 (OUTLIER) cc_final: 0.5615 (mp)
REVERT: C   21 ARG cc_start: 0.6302 (mmp-170) cc_final: 0.6047 (mmm160)
REVERT: C  129 PHE cc_start: 0.6960 (m-10) cc_final: 0.6538 (m-10)
REVERT: C  226 ASP cc_start: 0.7465 (p0) cc_final: 0.6792 (m-30)
REVERT: C  378 LYS cc_start: 0.8686 (tptp) cc_final: 0.8147 (tptp)
REVERT: B   15 TYR cc_start: 0.6469 (p90) cc_final: 0.6024 (p90)
REVERT: B   39 ARG cc_start: 0.4762 (ptt180) cc_final: 0.4535 (ptt180)
REVERT: B   80 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7547 (tt0)
REVERT: B  126 LYS cc_start: 0.7893 (mmmt) cc_final: 0.7517 (mmtm)
REVERT: B  165 ASN cc_start: 0.8193 (t0) cc_final: 0.7880 (t0)
  outliers start: 37
  outliers final: 24
  residues processed: 210
  average time/residue: 0.2927
  time to fit residues: 87.4851
Evaluate side-chains
  194 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 168
  time to evaluate  : 1.547 
-------------------------------------------------------------------------------
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  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  311 CYS
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  486 TYR
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  521 GLU
Chi-restraints excluded: chain A residue  543 ASN
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  918 ASN
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  933 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 C residue  271 THR
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 117 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 95 optimal weight:    0.2980
   chunk 164 optimal weight:    8.9990
   chunk 109 optimal weight:   10.0000
   chunk 154 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 132 optimal weight:    0.6980
   chunk 35 optimal weight:   10.0000
   chunk 140 optimal weight:    0.9980
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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 963 ASN
** C   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.221902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.151051 restraints weight = 18169.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3901 rms_B_bonded: 3.38
r_work: 0.3653 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3796
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3796 r_free = 0.3796    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 = 0.3796 r_free = 0.3796    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.3796
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.3816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  14496  Z= 0.200
  Angle     :  0.667  13.460  19731  Z= 0.347
  Chirality :  0.045   0.250   2183
  Planarity :  0.004   0.047   2397
  Dihedral  : 15.426 175.994   2172
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  : 10.11 %
    Favored  : 89.16 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 16.74 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.21), residues: 1642
  helix:  1.07 (0.22), residues: 560
  sheet: -0.26 (0.33), residues: 264
  loop : -2.46 (0.20), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C  37 
 HIS   0.003   0.001   HIS A 600 
 PHE   0.023   0.002   PHE A 200 
 TYR   0.018   0.002   TYR A 300 
 ARG   0.012   0.001   ARG C 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05230 (  495)
  hydrogen bonds       : angle       4.50119 ( 1404)
  covalent geometry    : bond        0.00483 (14496)
  covalent geometry    : angle       0.66726 (19731)

*********************** 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
  217 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 174
  time to evaluate  : 1.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 GLN cc_start: 0.6798 (tp40) cc_final: 0.6488 (tp40)
REVERT: A  218 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7527 (m-30)
REVERT: A  709 ASN cc_start: 0.8570 (t0) cc_final: 0.8033 (t0)
REVERT: A  875 ASP cc_start: 0.7169 (m-30) cc_final: 0.6918 (m-30)
REVERT: A  894 ARG cc_start: 0.7569 (ttp80) cc_final: 0.7133 (ttp80)
REVERT: A  895 MET cc_start: 0.7152 (ttp) cc_final: 0.6788 (ttp)
REVERT: A  922 ILE cc_start: 0.5993 (OUTLIER) cc_final: 0.5739 (mp)
REVERT: C  129 PHE cc_start: 0.7052 (m-10) cc_final: 0.6688 (m-10)
REVERT: C  226 ASP cc_start: 0.7636 (p0) cc_final: 0.7014 (t0)
REVERT: C  378 LYS cc_start: 0.8663 (tptp) cc_final: 0.8115 (tptp)
REVERT: B   15 TYR cc_start: 0.6513 (p90) cc_final: 0.5983 (p90)
REVERT: B  165 ASN cc_start: 0.8307 (t0) cc_final: 0.8027 (t0)
  outliers start: 43
  outliers final: 31
  residues processed: 209
  average time/residue: 0.2742
  time to fit residues: 83.8694
Evaluate side-chains
  197 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 164
  time to evaluate  : 1.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   26 ASN
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  170 HIS
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  311 CYS
Chi-restraints excluded: chain A residue  373 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  486 TYR
Chi-restraints excluded: chain A residue  521 GLU
Chi-restraints excluded: chain A residue  543 ASN
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  604 ARG
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  838 PHE
Chi-restraints excluded: chain A residue  910 LEU
Chi-restraints excluded: chain A residue  918 ASN
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain 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 C residue  413 ILE
Chi-restraints excluded: chain B residue  143 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 90 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 145 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 159 optimal weight:    8.9990
   chunk 56 optimal weight:    0.4980
   chunk 79 optimal weight:    3.9990
   chunk 101 optimal weight:    4.9990
   chunk 93 optimal weight:    0.0970
   overall best weight:    0.4778

-------------------------------------------------------------------------------
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 963 ASN
** C   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4685 r_free = 0.4685 target = 0.224807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.157620 restraints weight = 17723.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3998 rms_B_bonded: 3.03
r_work: 0.3728 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3866
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3866 r_free = 0.3866    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 = 0.3866 r_free = 0.3866    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.3866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.3842

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= 0.125
  Angle     :  0.609  11.419  19731  Z= 0.316
  Chirality :  0.042   0.238   2183
  Planarity :  0.004   0.047   2397
  Dihedral  : 15.349 175.435   2172
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  9.01 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 17.33 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.21), residues: 1642
  helix:  1.26 (0.23), residues: 559
  sheet: -0.33 (0.33), residues: 272
  loop : -2.37 (0.20), residues: 811

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  37 
 HIS   0.003   0.001   HIS B 181 
 PHE   0.024   0.001   PHE A 930 
 TYR   0.019   0.001   TYR A 668 
 ARG   0.007   0.000   ARG A 742 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04072 (  495)
  hydrogen bonds       : angle       4.34166 ( 1404)
  covalent geometry    : bond        0.00274 (14496)
  covalent geometry    : angle       0.60884 (19731)

*********************** 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
  201 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 166
  time to evaluate  : 1.439 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.7486 (mt-10) cc_final: 0.6404 (tp30)
REVERT: A  218 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7605 (m-30)
REVERT: A  859 MET cc_start: 0.2930 (pmm) cc_final: -0.1187 (mpp)
REVERT: A  875 ASP cc_start: 0.7161 (m-30) cc_final: 0.6917 (m-30)
REVERT: A  894 ARG cc_start: 0.7533 (ttp80) cc_final: 0.7162 (ttp80)
REVERT: A  895 MET cc_start: 0.7235 (ttp) cc_final: 0.6927 (ttp)
REVERT: A  922 ILE cc_start: 0.5935 (OUTLIER) cc_final: 0.5645 (mp)
REVERT: C   98 LEU cc_start: 0.6336 (OUTLIER) cc_final: 0.5943 (mm)
REVERT: C  129 PHE cc_start: 0.7067 (m-10) cc_final: 0.6695 (m-10)
REVERT: C  226 ASP cc_start: 0.7561 (p0) cc_final: 0.6951 (t0)
REVERT: C  378 LYS cc_start: 0.8660 (tptp) cc_final: 0.8139 (tptp)
REVERT: B   15 TYR cc_start: 0.6501 (p90) cc_final: 0.5955 (p90)
REVERT: B   80 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7523 (tt0)
REVERT: B  165 ASN cc_start: 0.8158 (t0) cc_final: 0.7876 (t0)
  outliers start: 35
  outliers final: 29
  residues processed: 195
  average time/residue: 0.2762
  time to fit residues: 78.0608
Evaluate side-chains
  192 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 160
  time to evaluate  : 1.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  170 HIS
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  311 CYS
Chi-restraints excluded: chain A residue  373 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  486 TYR
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  521 GLU
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  604 ARG
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  838 PHE
Chi-restraints excluded: chain A residue  910 LEU
Chi-restraints excluded: chain A residue  918 ASN
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain C residue   98 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 C residue  271 THR
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 70 optimal weight:    6.9990
   chunk 103 optimal weight:    5.9990
   chunk 85 optimal weight:    0.8980
   chunk 41 optimal weight:    0.2980
   chunk 23 optimal weight:    3.9990
   chunk 123 optimal weight:    0.6980
   chunk 136 optimal weight:    0.4980
   chunk 55 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 146 optimal weight:    0.0980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.4697 r_free = 0.4697 target = 0.226096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.159948 restraints weight = 18159.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.4019 rms_B_bonded: 3.31
r_work: 0.3739 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3877
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3877 r_free = 0.3877    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 = 0.3877 r_free = 0.3877    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.3877
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.3939

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= 0.124
  Angle     :  0.607  10.561  19731  Z= 0.314
  Chirality :  0.042   0.230   2183
  Planarity :  0.004   0.046   2397
  Dihedral  : 15.312 175.310   2172
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  9.50 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 17.20 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.21), residues: 1642
  helix:  1.35 (0.23), residues: 553
  sheet: -0.14 (0.34), residues: 264
  loop : -2.37 (0.20), residues: 825

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 212 
 HIS   0.005   0.001   HIS B   8 
 PHE   0.023   0.001   PHE A 930 
 TYR   0.018   0.001   TYR A 658 
 ARG   0.008   0.000   ARG A 742 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03957 (  495)
  hydrogen bonds       : angle       4.27013 ( 1404)
  covalent geometry    : bond        0.00273 (14496)
  covalent geometry    : angle       0.60670 (19731)

*********************** 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
  205 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 165
  time to evaluate  : 1.542 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.7455 (mt-10) cc_final: 0.6303 (tp30)
REVERT: A   70 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6945 (pt0)
REVERT: A  218 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7535 (m-30)
REVERT: A  859 MET cc_start: 0.2869 (pmm) cc_final: -0.0912 (mtp)
REVERT: A  875 ASP cc_start: 0.7148 (m-30) cc_final: 0.6922 (m-30)
REVERT: A  894 ARG cc_start: 0.7308 (ttp80) cc_final: 0.6906 (ttp80)
REVERT: A  895 MET cc_start: 0.7055 (ttp) cc_final: 0.6804 (ttp)
REVERT: A  922 ILE cc_start: 0.5764 (OUTLIER) cc_final: 0.5468 (mp)
REVERT: A  951 GLU cc_start: 0.5739 (tp30) cc_final: 0.4859 (mp0)
REVERT: C   98 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.5969 (mm)
REVERT: C  129 PHE cc_start: 0.7116 (m-10) cc_final: 0.6868 (m-10)
REVERT: C  226 ASP cc_start: 0.7528 (p0) cc_final: 0.6887 (t0)
REVERT: C  378 LYS cc_start: 0.8650 (tptp) cc_final: 0.8117 (tptp)
REVERT: B   15 TYR cc_start: 0.6440 (p90) cc_final: 0.5957 (p90)
REVERT: B  165 ASN cc_start: 0.8187 (t0) cc_final: 0.7893 (t0)
REVERT: B  212 TRP cc_start: 0.6960 (m100) cc_final: 0.6677 (m100)
  outliers start: 40
  outliers final: 32
  residues processed: 197
  average time/residue: 0.2862
  time to fit residues: 81.3396
Evaluate side-chains
  196 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 160
  time to evaluate  : 1.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   70 GLU
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  170 HIS
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  311 CYS
Chi-restraints excluded: chain A residue  373 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  486 TYR
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  521 GLU
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  604 ARG
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  838 PHE
Chi-restraints excluded: chain A residue  910 LEU
Chi-restraints excluded: chain A residue  918 ASN
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  130 VAL
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 C residue  271 THR
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 105 optimal weight:    1.9990
   chunk 147 optimal weight:    0.9980
   chunk 81 optimal weight:    8.9990
   chunk 130 optimal weight:    0.4980
   chunk 60 optimal weight:    0.3980
   chunk 39 optimal weight:    0.0270
   chunk 73 optimal weight:    0.5980
   chunk 114 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 94 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.4638

-------------------------------------------------------------------------------
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 = 0.4699 r_free = 0.4699 target = 0.226396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.162722 restraints weight = 18161.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.4061 rms_B_bonded: 3.07
r_work: 0.3748 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3748
-------------------------------------------------------------------------------
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: 0.7292
moved from start:          0.4011

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= 0.124
  Angle     :  0.612  12.558  19731  Z= 0.315
  Chirality :  0.042   0.249   2183
  Planarity :  0.004   0.046   2397
  Dihedral  : 15.277 175.262   2172
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  9.44 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 17.20 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.21), residues: 1642
  helix:  1.34 (0.23), residues: 554
  sheet: -0.19 (0.33), residues: 269
  loop : -2.36 (0.20), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 212 
 HIS   0.003   0.001   HIS A 839 
 PHE   0.024   0.001   PHE A 930 
 TYR   0.019   0.001   TYR A 658 
 ARG   0.009   0.000   ARG A 742 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03897 (  495)
  hydrogen bonds       : angle       4.25890 ( 1404)
  covalent geometry    : bond        0.00276 (14496)
  covalent geometry    : angle       0.61156 (19731)

********************** 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
  201 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 164
  time to evaluate  : 1.514 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.7495 (mt-10) cc_final: 0.6312 (tp30)
REVERT: A  218 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7532 (m-30)
REVERT: A  859 MET cc_start: 0.2791 (pmm) cc_final: -0.0828 (mtp)
REVERT: A  875 ASP cc_start: 0.7181 (m-30) cc_final: 0.6960 (m-30)
REVERT: A  894 ARG cc_start: 0.7354 (ttp80) cc_final: 0.6928 (ttp80)
REVERT: A  895 MET cc_start: 0.7047 (ttp) cc_final: 0.6814 (ttp)
REVERT: A  922 ILE cc_start: 0.5817 (OUTLIER) cc_final: 0.5497 (mp)
REVERT: C   21 ARG cc_start: 0.5733 (mmp-170) cc_final: 0.5496 (mmp-170)
REVERT: C   98 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.6017 (mm)
REVERT: C  129 PHE cc_start: 0.7208 (m-10) cc_final: 0.6957 (m-10)
REVERT: C  166 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7354 (mp)
REVERT: C  226 ASP cc_start: 0.7481 (p0) cc_final: 0.6760 (m-30)
REVERT: C  292 ARG cc_start: 0.8743 (tmm-80) cc_final: 0.8505 (tmm-80)
REVERT: C  378 LYS cc_start: 0.8659 (tptp) cc_final: 0.8133 (tptp)
REVERT: B   15 TYR cc_start: 0.6432 (p90) cc_final: 0.5942 (p90)
REVERT: B  165 ASN cc_start: 0.8202 (t0) cc_final: 0.7893 (t0)
REVERT: B  212 TRP cc_start: 0.7047 (m100) cc_final: 0.6796 (m100)
  outliers start: 37
  outliers final: 32
  residues processed: 193
  average time/residue: 0.3489
  time to fit residues: 97.9338
Evaluate side-chains
  195 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 159
  time to evaluate  : 2.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  170 HIS
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  311 CYS
Chi-restraints excluded: chain A residue  373 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  486 TYR
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  707 LEU
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  838 PHE
Chi-restraints excluded: chain A residue  910 LEU
Chi-restraints excluded: chain A residue  918 ASN
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  933 ILE
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain C residue  162 ILE
Chi-restraints excluded: chain C residue  166 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 C residue  271 THR
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9980
   chunk 21 optimal weight:    0.4980
   chunk 122 optimal weight:    8.9990
   chunk 164 optimal weight:    7.9990
   chunk 107 optimal weight:    7.9990
   chunk 113 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 127 optimal weight:   10.0000
   chunk 157 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4684 r_free = 0.4684 target = 0.224641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.159875 restraints weight = 18213.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.4023 rms_B_bonded: 3.16
r_work: 0.3720 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3858
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3858 r_free = 0.3858    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 = 0.3858 r_free = 0.3858    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.3858
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.4144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  14496  Z= 0.150
  Angle     :  0.641  13.153  19731  Z= 0.329
  Chirality :  0.043   0.198   2183
  Planarity :  0.004   0.045   2397
  Dihedral  : 15.298 175.411   2172
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  9.44 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.33 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.21), residues: 1642
  helix:  1.27 (0.23), residues: 554
  sheet: -0.18 (0.34), residues: 264
  loop : -2.37 (0.20), residues: 824

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 212 
 HIS   0.004   0.001   HIS B   8 
 PHE   0.021   0.002   PHE A 930 
 TYR   0.019   0.001   TYR A 723 
 ARG   0.004   0.000   ARG A 742 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04408 (  495)
  hydrogen bonds       : angle       4.31840 ( 1404)
  covalent geometry    : bond        0.00350 (14496)
  covalent geometry    : angle       0.64113 (19731)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11080.33 seconds
wall clock time: 193 minutes 39.44 seconds (11619.44 seconds total)