Starting phenix.real_space_refine
on Fri Jul  3 11:27:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k8s_36960/07_2026/8k8s_36960.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k8s_36960/07_2026/8k8s_36960.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k8s_36960/07_2026/8k8s_36960.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k8s_36960/07_2026/8k8s_36960.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k8s_36960/07_2026/8k8s_36960.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k8s_36960/07_2026/8k8s_36960.cif"
  }
  resolution = 3.06
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.111
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      29      5.49       5
     Mg      1      5.21       5
     S      71      5.16       5
     C    8855      2.51       5
     N    2327      2.21       5
     O    2679      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 114 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13962
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 8201
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1004, 8201
          Classifications: {'peptide': 1004}
          Link IDs: {'PTRANS': 37, 'TRANS': 966}
    Chain: "B"
      Number of atoms: 1772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1772
          Classifications: {'peptide': 218}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204}
    Chain: "C"
      Number of atoms: 3406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 418, 3406
          Classifications: {'peptide': 418}
          Link IDs: {'PTRANS': 10, 'TRANS': 407}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 231
          Classifications: {'DNA': 12}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 11}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 321
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 31
          Unusual residues: {' MG': 1, 'HF4': 1}
          Classifications: {'undetermined': 2, 'water': 1}
          Link IDs: {None: 2}
  Time building chain proxies: 2.60, per 1000 atoms: 0.19
  Number of scatterers: 13962
  At special positions: 0
  Unit cell: (102.178, 129.353, 145.658, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      71     16.00
     P      29     15.00
     Mg      1     11.99
     O    2679      8.00
     N    2327      7.00
     C    8855      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 434.2 milliseconds
  

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3142

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 20 sheets defined
      39.1% alpha, 22.0% beta
      11 base pairs and 22 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 48
    Processing helix  chain 'A' and resid 108 through 116
    Processing helix  chain 'A' and resid 144 through 148
      removed outlier: 3.651A  pdb=" N   ASN A 147 " --> pdb=" O   ASP A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    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 337
    Processing helix  chain 'A' and resid 345 through 354
    Processing helix  chain 'A' and resid 380 through 390
      removed outlier: 3.514A  pdb=" N   VAL A 388 " --> pdb=" O   THR A 384 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   THR A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 444
    Processing helix  chain 'A' and resid 448 through 473
      removed outlier: 3.513A  pdb=" N   TYR A 458 " --> pdb=" O   ASP A 454 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   CYS A 466 " --> pdb=" O   ASP A 462 " (cutoff:3.500A)
      removed outlier: 4.074A  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 489 through 493
    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 561
    Processing helix  chain 'A' and resid 576 through 591
      removed outlier: 3.896A  pdb=" N   GLU A 581 " --> pdb=" O   ARG A 577 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLN A 589 " --> pdb=" O   GLN A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 642
      removed outlier: 3.993A  pdb=" N   ARG A 625 " --> pdb=" O   GLY A 621 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 646 through 670
      removed outlier: 3.813A  pdb=" N   ALA A 651 " --> pdb=" O   SER A 647 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   TYR A 668 " --> pdb=" O   ALA A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 703
    Processing helix  chain 'A' and resid 763 through 782
      removed outlier: 3.654A  pdb=" N   SER A 767 " --> pdb=" O   ASP A 763 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ILE A 768 " --> pdb=" O   VAL A 764 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 837 through 857
      removed outlier: 3.723A  pdb=" N   ASN A 841 " --> pdb=" O   LYS A 837 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 883
    Processing helix  chain 'A' and resid 886 through 890
    Processing helix  chain 'A' and resid 905 through 918
    Processing helix  chain 'A' and resid 947 through 949
      No H-bonds generated for 'chain 'A' and resid 947 through 949'
    Processing helix  chain 'A' and resid 967 through 981
      removed outlier: 3.787A  pdb=" N   TYR A 971 " --> pdb=" O   PHE A 967 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 987 through 997
    Processing helix  chain 'B' and resid 16 through 21
      Proline residue:  B  21  - end of helix
    Processing helix  chain 'B' and resid 22 through 38
      removed outlier: 3.740A  pdb=" N   VAL B  33 " --> pdb=" O   PHE B  29 " (cutoff:3.500A)
      removed outlier: 5.553A  pdb=" N   SER B  35 " --> pdb=" O   ASN B  31 " (cutoff:3.500A)
      removed outlier: 5.596A  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 86 through 101
    Processing helix  chain 'B' and resid 110 through 113
      removed outlier: 3.638A  pdb=" N   ILE B 113 " --> pdb=" O   LEU B 110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 110 through 113'
    Processing helix  chain 'B' and resid 137 through 150
    Processing helix  chain 'B' and resid 165 through 170
      removed outlier: 3.746A  pdb=" N   LEU B 170 " --> pdb=" O   ARG B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 192
      removed outlier: 4.165A  pdb=" N   HIS B 187 " --> pdb=" O   ALA B 184 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLN B 188 " --> pdb=" O   ARG B 185 " (cutoff:3.500A)
      removed outlier: 5.769A  pdb=" N   PHE B 189 " --> pdb=" O   ASP B 186 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLU B 190 " --> pdb=" O   HIS B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 205
      removed outlier: 3.536A  pdb=" N   ASN B 199 " --> pdb=" O   PHE B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 214
    Processing helix  chain 'C' and resid 3 through 19
    Processing helix  chain 'C' and resid 27 through 43
    Processing helix  chain 'C' and resid 57 through 61
    Processing helix  chain 'C' and resid 107 through 121
    Processing helix  chain 'C' and resid 149 through 159
    Processing helix  chain 'C' and resid 177 through 187
    Processing helix  chain 'C' and resid 249 through 257
      removed outlier: 4.274A  pdb=" N   LEU C 253 " --> pdb=" O   ASP C 249 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 298
    Processing helix  chain 'C' and resid 315 through 323
    Processing helix  chain 'C' and resid 330 through 332
      No H-bonds generated for 'chain 'C' and resid 330 through 332'
    Processing helix  chain 'C' and resid 333 through 339
      removed outlier: 3.611A  pdb=" N   ASN C 339 " --> pdb=" O   VAL C 335 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 344 through 349
      removed outlier: 3.638A  pdb=" N   ILE C 348 " --> pdb=" O   VAL C 344 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 352 through 360
    Processing helix  chain 'C' and resid 365 through 373
    Processing helix  chain 'C' and resid 391 through 396
      removed outlier: 3.826A  pdb=" N   ASN C 396 " --> pdb=" O   ASN C 393 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 397 through 406
      removed outlier: 3.652A  pdb=" N   ASN C 406 " --> pdb=" O   THR C 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 425
      removed outlier: 4.119A  pdb=" N   PHE C 410 " --> pdb=" O   ASN C 406 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ARG C 423 " --> pdb=" O   ASP C 419 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10
      removed outlier: 5.775A  pdb=" N   CYS A   5 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ARG A  23 " --> pdb=" O   CYS A   5 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   CYS A 139 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43
      removed outlier: 4.117A  pdb=" N   GLY A  61 " --> pdb=" O   MET A  88 " (cutoff:3.500A)
      removed outlier: 5.617A  pdb=" N   LEU A  90 " --> pdb=" O   PRO A  59 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   GLU A  92 " --> pdb=" O   ALA A  57 " (cutoff:3.500A)
      removed outlier: 5.544A  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: 6.568A  pdb=" N   ILE A 614 " --> pdb=" O   VAL A 569 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   VAL A 571 " --> pdb=" O   ILE A 612 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   ILE A 612 " --> pdb=" O   VAL A 571 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   VAL A 573 " --> pdb=" O   SER A 610 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   SER A 610 " --> pdb=" O   VAL A 573 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   GLU A 611 " --> pdb=" O   CYS A 601 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223
      removed outlier: 6.628A  pdb=" N   LEU A 222 " --> pdb=" O   LEU A 238 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   SER A 184 " --> pdb=" O   ASN A 204 " (cutoff:3.500A)
      removed outlier: 6.328A  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 305
    Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 363
      removed outlier: 5.526A  pdb=" N   VAL A 360 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   ILE A 371 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASN A 362 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   LYS A 416 " --> pdb=" O   LYS A 408 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   LYS A 408 " --> pdb=" O   LYS A 416 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   VAL A 418 " --> pdb=" O   ILE A 406 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 732 through 734
      removed outlier: 6.868A  pdb=" N   PHE A 756 " --> pdb=" O   VAL A 748 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   GLY A 750 " --> pdb=" O   SER A 754 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   SER A 754 " --> pdb=" O   GLY A 750 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   ALA A 793 " --> pdb=" O   ILE A 547 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   ASP A 549 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   PHE A 791 " --> pdb=" O   ASP A 549 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   LEU A 798 " --> pdb=" O   THR A 807 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   THR A 807 " --> pdb=" O   LEU A 798 " (cutoff:3.500A)
      removed outlier: 4.949A  pdb=" N   MET A 800 " --> pdb=" O   LYS A 805 " (cutoff:3.500A)
      removed outlier: 7.575A  pdb=" N   LYS A 805 " --> pdb=" O   MET A 800 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 892 through 895
      removed outlier: 4.603A  pdb=" N   TYR A 929 " --> pdb=" O   ILE A 954 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 895
    Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 5
    Processing sheet with id=AB3, first strand: chain 'B' and resid 42 through 43
    Processing sheet with id=AB4, first strand: chain 'B' and resid 115 through 120
      removed outlier: 6.784A  pdb=" N   GLY B 115 " --> pdb=" O   LYS B  60 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   ARG B  61 " --> pdb=" O   VAL B 154 " (cutoff:3.500A)
      removed outlier: 7.722A  pdb=" N   TYR B 156 " --> pdb=" O   ARG B  61 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   CYS B  63 " --> pdb=" O   TYR B 156 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   LEU B 158 " --> pdb=" O   CYS B  63 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   CYS B  65 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 107 through 108
    Processing sheet with id=AB6, first strand: chain 'C' and resid 64 through 65
    Processing sheet with id=AB7, first strand: chain 'C' and resid 95 through 97
    Processing sheet with id=AB8, first strand: chain 'C' and resid 95 through 97
      removed outlier: 7.045A  pdb=" N   ILE C 142 " --> pdb=" O   ASP C 125 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 244 through 245
      removed outlier: 3.602A  pdb=" N   VAL C 237 " --> pdb=" O   ILE C 245 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   THR C 262 " --> pdb=" O   ILE C 220 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 304
    Processing sheet with id=AC2, first strand: chain 'C' and resid 375 through 380
      removed outlier: 3.586A  pdb=" N   ASN C 386 " --> pdb=" O   LYS C 378 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   GLU C 380 " --> pdb=" O   VAL C 384 " (cutoff:3.500A)
      removed outlier: 5.251A  pdb=" N   VAL C 384 " --> pdb=" O   GLU C 380 " (cutoff:3.500A)

    595 hydrogen bonds defined for protein.
    1656 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      29 hydrogen bonds
      58 hydrogen bond angles
      0 basepair planarities
      11 basepair parallelities
      22 stacking parallelities
  Total time for adding SS restraints: 2.20

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 2226
        1.31 -     1.43: 3915
        1.43 -     1.56: 8011
        1.56 -     1.68: 58
        1.68 -     1.81: 108
  Bond restraints: 14318
  Sorted by residual:
  bond pdb=" C3' HF4 A1102 "
       pdb=" C4' HF4 A1102 "
    ideal  model  delta    sigma   weight residual
    1.531  1.342  0.189 2.00e-02 2.50e+03 8.90e+01
  bond pdb=" C4' HF4 A1102 "
       pdb=" O4' HF4 A1102 "
    ideal  model  delta    sigma   weight residual
    1.427  1.600 -0.173 2.00e-02 2.50e+03 7.52e+01
  bond pdb=" C5  HF4 A1102 "
       pdb=" C6  HF4 A1102 "
    ideal  model  delta    sigma   weight residual
    1.349  1.493 -0.144 2.00e-02 2.50e+03 5.19e+01
  bond pdb=" C2  HF4 A1102 "
       pdb=" N3  HF4 A1102 "
    ideal  model  delta    sigma   weight residual
    1.348  1.472 -0.124 2.00e-02 2.50e+03 3.84e+01
  bond pdb=" C4  HF4 A1102 "
       pdb=" N3  HF4 A1102 "
    ideal  model  delta    sigma   weight residual
    1.319  1.435 -0.116 2.00e-02 2.50e+03 3.39e+01
  ... (remaining 14313 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 19237
        2.52 -     5.04: 217
        5.04 -     7.56: 10
        7.56 -    10.08: 2
       10.08 -    12.60: 2
  Bond angle restraints: 19468
  Sorted by residual:
  angle pdb=" N   GLY A 570 "
        pdb=" CA  GLY A 570 "
        pdb=" C   GLY A 570 "
      ideal   model   delta    sigma   weight residual
     110.63  117.99   -7.36 1.45e+00 4.76e-01 2.58e+01
  angle pdb=" N3   DT E  18 "
        pdb=" C4   DT E  18 "
        pdb=" O4   DT E  18 "
      ideal   model   delta    sigma   weight residual
     119.90  122.61   -2.71 6.00e-01 2.78e+00 2.04e+01
  angle pdb=" O4'  DT E  23 "
        pdb=" C4'  DT E  23 "
        pdb=" C3'  DT E  23 "
      ideal   model   delta    sigma   weight residual
     106.00  103.39    2.61 6.00e-01 2.78e+00 1.89e+01
  angle pdb=" O3A HF4 A1102 "
        pdb=" PB  HF4 A1102 "
        pdb=" O3B HF4 A1102 "
      ideal   model   delta    sigma   weight residual
      97.36  109.96  -12.60 3.00e+00 1.11e-01 1.77e+01
  angle pdb=" N3   DT F  15 "
        pdb=" C4   DT F  15 "
        pdb=" O4   DT F  15 "
      ideal   model   delta    sigma   weight residual
     119.90  122.39   -2.49 6.00e-01 2.78e+00 1.73e+01
  ... (remaining 19463 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.86: 8297
       26.86 -    53.72: 246
       53.72 -    80.59: 48
       80.59 -   107.45: 9
      107.45 -   134.31: 2
  Dihedral angle restraints: 8602
    sinusoidal: 3733
      harmonic: 4869
  Sorted by residual:
  dihedral pdb=" C5' HF4 A1102 "
           pdb=" O5' HF4 A1102 "
           pdb=" PA  HF4 A1102 "
           pdb=" O1A HF4 A1102 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -166.00  -31.69 -134.31     1      3.00e+01 1.11e-03 1.81e+01
  dihedral pdb=" C5' HF4 A1102 "
           pdb=" O5' HF4 A1102 "
           pdb=" PA  HF4 A1102 "
           pdb=" O2A HF4 A1102 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -34.81 -151.24  116.43     1      3.00e+01 1.11e-03 1.54e+01
  dihedral pdb=" CA  SER A 836 "
           pdb=" C   SER A 836 "
           pdb=" N   LYS A 837 "
           pdb=" CA  LYS A 837 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.57   19.43     0      5.00e+00 4.00e-02 1.51e+01
  ... (remaining 8599 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1646
       0.061 -    0.122: 380
       0.122 -    0.183: 125
       0.183 -    0.244: 3
       0.244 -    0.305: 1
  Chirality restraints: 2155
  Sorted by residual:
  chirality pdb=" C3' HF4 A1102 "
            pdb=" C2' HF4 A1102 "
            pdb=" C4' HF4 A1102 "
            pdb=" O3' HF4 A1102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.42   -0.30 2.00e-01 2.50e+01 2.32e+00
  chirality pdb=" CA  VAL A 794 "
            pdb=" N   VAL A 794 "
            pdb=" C   VAL A 794 "
            pdb=" CB  VAL A 794 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 9.36e-01
  chirality pdb=" CA  VAL A 259 "
            pdb=" N   VAL A 259 "
            pdb=" C   VAL A 259 "
            pdb=" CB  VAL A 259 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 9.22e-01
  ... (remaining 2152 not shown)

  Planarity restraints: 2376
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 289 "    0.011 2.00e-02 2.50e+03   2.13e-02 4.53e+00
        pdb=" C   VAL C 289 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   VAL C 289 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ILE C 290 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B  20 "   -0.028 5.00e-02 4.00e+02   4.19e-02 2.80e+00
        pdb=" N   PRO B  21 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B  21 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  21 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 502 "   -0.006 2.00e-02 2.50e+03   1.21e-02 1.46e+00
        pdb=" C   ILE A 502 "    0.021 2.00e-02 2.50e+03
        pdb=" O   ILE A 502 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   LYS A 503 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 2373 not shown)

  Histogram of nonbonded interaction distances:
        1.84 -     2.45: 13
        2.45 -     3.07: 8987
        3.07 -     3.68: 19549
        3.68 -     4.29: 31716
        4.29 -     4.90: 50834
  Nonbonded interactions: 111099
  Sorted by model distance:
  nonbonded pdb="MG    MG A1101 "
            pdb=" O1B HF4 A1102 "
     model   vdw
     1.842 2.170
  nonbonded pdb=" OD2 ASP A 753 "
            pdb="MG    MG A1101 "
     model   vdw
     1.847 2.170
  nonbonded pdb=" O   TYR A 550 "
            pdb="MG    MG A1101 "
     model   vdw
     2.008 2.170
  nonbonded pdb="MG    MG A1101 "
            pdb=" O1G HF4 A1102 "
     model   vdw
     2.284 2.170
  nonbonded pdb=" OD1 ASP A 549 "
            pdb="MG    MG A1101 "
     model   vdw
     2.350 2.170
  ... (remaining 111094 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=1.00 max=1.00 mean=1.00
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:             1.460
  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:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.140
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:0.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6864
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      :  0.010   0.189  14318  Z= 0.534
  Angle     :  0.736  12.604  19468  Z= 0.485
  Chirality :  0.056   0.305   2155
  Planarity :  0.003   0.042   2376
  Dihedral  : 12.912 134.310   5460
  Min Nonbonded Distance : 1.842

Molprobity Statistics.
  All-atom Clashscore : 0.87
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.19 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.20), residues: 1631
  helix: -0.14 (0.20), residues: 546
  sheet:  0.02 (0.27), residues: 354
  loop : -0.43 (0.23), residues: 731

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 625 
 TYR   0.001   0.000   TYR A 653 
 PHE   0.001   0.000   PHE A 630 
 TRP   0.001   0.000   TRP B  19 
 HIS   0.001   0.000   HIS A 141 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00967 /  0.53 (14318)
  covalent geometry    : angle       0.73603 /  0.49 (19468)
  hydrogen bonds       : bond        0.21564 / 14.79 (  612)
  hydrogen bonds       : angle       6.76417 /  4.75 ( 1714)

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

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

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  407 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 407
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  462 ASP cc_start: 0.7898 (m-30) cc_final: 0.7556 (m-30)
REVERT: A  534 PHE cc_start: 0.8316 (m-80) cc_final: 0.8032 (m-10)
REVERT: A  753 ASP cc_start: 0.7862 (t0) cc_final: 0.7265 (p0)
REVERT: A  797 ASN cc_start: 0.7580 (m-40) cc_final: 0.7222 (t0)
REVERT: B   48 LYS cc_start: 0.7603 (mmtt) cc_final: 0.7315 (mttm)
REVERT: C   32 ASN cc_start: 0.6408 (m-40) cc_final: 0.6098 (m-40)
REVERT: C  228 ILE cc_start: 0.6451 (pt) cc_final: 0.6229 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 407
  average time/residue: 0.1153
  time to fit residues: 65.1215
Evaluate side-chains
  216 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.0970
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.0060
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    5.9990
   overall best weight:    0.5394

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 HIS
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 839 HIS
C 134 ASN
C 415 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.231639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.185516 restraints weight = 16128.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.4114 rms_B_bonded: 4.11
r_work: 0.3583 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.2587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14318  Z= 0.158
  Angle     :  0.616   7.696  19468  Z= 0.338
  Chirality :  0.044   0.231   2155
  Planarity :  0.004   0.044   2376
  Dihedral  : 14.224 132.133   2136
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.64 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  7.85 %
    Favored  : 90.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.21), residues: 1631
  helix:  0.87 (0.21), residues: 562
  sheet:  0.24 (0.28), residues: 341
  loop : -0.45 (0.23), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 292 
 TYR   0.019   0.002   TYR A 971 
 PHE   0.026   0.002   PHE A 838 
 TRP   0.009   0.001   TRP A 470 
 HIS   0.010   0.001   HIS A 839 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.16 (14318)
  covalent geometry    : angle       0.61554 /  0.34 (19468)
  hydrogen bonds       : bond        0.06330 /  4.32 (  612)
  hydrogen bonds       : angle       4.90864 /  3.45 ( 1714)

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

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

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 240
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.7372 (tp30) cc_final: 0.6997 (pt0)
REVERT: A  131 TYR cc_start: 0.7214 (m-80) cc_final: 0.6931 (m-80)
REVERT: A  257 ASP cc_start: 0.8295 (m-30) cc_final: 0.8082 (m-30)
REVERT: A  387 LYS cc_start: 0.7176 (ttpp) cc_final: 0.6795 (ttpt)
REVERT: A  404 LYS cc_start: 0.8297 (tttt) cc_final: 0.7909 (tmtt)
REVERT: A  709 ASN cc_start: 0.8342 (p0) cc_final: 0.7933 (p0)
REVERT: A  819 SER cc_start: 0.8551 (m) cc_final: 0.8291 (t)
REVERT: A  842 MET cc_start: 0.7641 (mpp) cc_final: 0.7217 (mpp)
REVERT: B   32 GLU cc_start: 0.6892 (tt0) cc_final: 0.6651 (tt0)
REVERT: C   32 ASN cc_start: 0.6160 (m-40) cc_final: 0.5841 (m-40)
REVERT: C   95 MET cc_start: 0.6199 (tpp) cc_final: 0.5842 (tpp)
REVERT: C  317 LYS cc_start: 0.8772 (tttt) cc_final: 0.8133 (mmtm)
REVERT: C  375 MET cc_start: 0.5947 (ttm) cc_final: 0.5729 (ttm)
  outliers start: 21
  outliers final: 17
  residues processed: 257
  average time/residue: 0.1074
  time to fit residues: 39.4923
Evaluate side-chains
  203 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 186
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ASN
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  403 CYS
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  764 VAL
Chi-restraints excluded: chain A residue  976 THR
Chi-restraints excluded: chain B residue   17 ASP
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue  251 ASP
Chi-restraints excluded: chain C residue  394 CYS
Chi-restraints excluded: chain C residue  408 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 63 optimal weight:    0.4980
   chunk 58 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 80 optimal weight:    5.9990
   chunk 133 optimal weight:    0.0870
   chunk 97 optimal weight:    8.9990
   chunk 59 optimal weight:    2.9990
   chunk 103 optimal weight:    0.8980
   chunk 109 optimal weight:    0.0050
   overall best weight:    0.4372

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 225 GLN
B  59 ASN
C 374 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.230619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.184401 restraints weight = 16185.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.4108 rms_B_bonded: 3.99
r_work: 0.3584 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.3165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  14318  Z= 0.121
  Angle     :  0.525   8.585  19468  Z= 0.290
  Chirality :  0.042   0.158   2155
  Planarity :  0.004   0.054   2376
  Dihedral  : 13.907 135.120   2136
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  9.17 %
    Favored  : 89.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.21), residues: 1631
  helix:  1.03 (0.22), residues: 563
  sheet:  0.26 (0.28), residues: 342
  loop : -0.45 (0.23), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  16 
 TYR   0.020   0.001   TYR C 301 
 PHE   0.017   0.001   PHE A 838 
 TRP   0.009   0.001   TRP A 470 
 HIS   0.006   0.001   HIS A 839 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.12 (14318)
  covalent geometry    : angle       0.52496 /  0.29 (19468)
  hydrogen bonds       : bond        0.05139 /  3.52 (  612)
  hydrogen bonds       : angle       4.59795 /  3.23 ( 1714)

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

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

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 206
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 TYR cc_start: 0.7248 (m-80) cc_final: 0.6985 (m-80)
REVERT: A  192 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.7168 (m-30)
REVERT: A  387 LYS cc_start: 0.7219 (ttpp) cc_final: 0.6843 (ttpt)
REVERT: A  404 LYS cc_start: 0.8334 (tttt) cc_final: 0.7931 (tmtt)
REVERT: A  534 PHE cc_start: 0.8632 (m-80) cc_final: 0.8360 (m-80)
REVERT: A  709 ASN cc_start: 0.8190 (p0) cc_final: 0.7882 (p0)
REVERT: A  725 ASP cc_start: 0.6315 (t0) cc_final: 0.5920 (p0)
REVERT: A  819 SER cc_start: 0.8588 (m) cc_final: 0.8330 (t)
REVERT: A  996 MET cc_start: 0.7326 (tpt) cc_final: 0.6207 (tpt)
REVERT: B  126 LYS cc_start: 0.8006 (ttmt) cc_final: 0.7548 (tptp)
REVERT: C   32 ASN cc_start: 0.6171 (m-40) cc_final: 0.5865 (m-40)
REVERT: C   95 MET cc_start: 0.6402 (tpp) cc_final: 0.5949 (tpp)
REVERT: C  118 LEU cc_start: 0.2719 (OUTLIER) cc_final: 0.2508 (mp)
  outliers start: 26
  outliers final: 16
  residues processed: 223
  average time/residue: 0.1252
  time to fit residues: 40.6537
Evaluate side-chains
  194 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 176
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ASN
Chi-restraints excluded: chain A residue   79 LYS
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  403 CYS
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  610 SER
Chi-restraints excluded: chain A residue  753 ASP
Chi-restraints excluded: chain B residue   17 ASP
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  394 CYS
Chi-restraints excluded: chain C residue  408 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 7 optimal weight:    0.0970
   chunk 157 optimal weight:    2.9990
   chunk 132 optimal weight:   40.0000
   chunk 158 optimal weight:    0.4980
   chunk 95 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 139 optimal weight:   30.0000
   chunk 103 optimal weight:    1.9990
   chunk 143 optimal weight:    9.9990
   chunk 119 optimal weight:    9.9990
   chunk 156 optimal weight:    4.9990
   overall best weight:    1.2782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 915 ASN
B  52 GLN
B  59 ASN
B 111 ASN
** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.226913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.171636 restraints weight = 16117.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3961 rms_B_bonded: 1.95
r_work: 0.3649 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3509 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.3538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.104  14318  Z= 0.159
  Angle     :  0.559   8.249  19468  Z= 0.302
  Chirality :  0.044   0.244   2155
  Planarity :  0.004   0.057   2376
  Dihedral  : 13.970 136.330   2136
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  :  9.11 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.21), residues: 1631
  helix:  0.90 (0.22), residues: 561
  sheet:  0.12 (0.28), residues: 341
  loop : -0.60 (0.23), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 167 
 TYR   0.028   0.002   TYR A 554 
 PHE   0.016   0.002   PHE A 838 
 TRP   0.013   0.002   TRP C  43 
 HIS   0.006   0.001   HIS A 839 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00363 /  0.16 (14318)
  covalent geometry    : angle       0.55893 /  0.30 (19468)
  hydrogen bonds       : bond        0.05079 /  3.46 (  612)
  hydrogen bonds       : angle       4.56012 /  3.20 ( 1714)

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

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

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 183
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
REVERT: A  131 TYR cc_start: 0.7371 (m-80) cc_final: 0.7009 (m-80)
REVERT: A  147 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7254 (t0)
REVERT: A  313 MET cc_start: 0.6929 (mmt) cc_final: 0.6111 (mmt)
REVERT: A  387 LYS cc_start: 0.7263 (ttpp) cc_final: 0.6879 (ttpt)
REVERT: A  404 LYS cc_start: 0.8430 (tttt) cc_final: 0.8009 (tmtt)
REVERT: A  656 MET cc_start: 0.8452 (mtp) cc_final: 0.7966 (mtp)
REVERT: A  709 ASN cc_start: 0.8253 (p0) cc_final: 0.7981 (p0)
REVERT: A  725 ASP cc_start: 0.6495 (t0) cc_final: 0.5925 (p0)
REVERT: A  819 SER cc_start: 0.8629 (m) cc_final: 0.8369 (t)
REVERT: A  996 MET cc_start: 0.7315 (tpt) cc_final: 0.6965 (tpp)
REVERT: B  126 LYS cc_start: 0.8171 (ttmt) cc_final: 0.7668 (tptp)
REVERT: C   32 ASN cc_start: 0.6345 (m-40) cc_final: 0.6056 (m-40)
REVERT: C  118 LEU cc_start: 0.2581 (OUTLIER) cc_final: 0.2333 (mp)
REVERT: C  184 MET cc_start: 0.5854 (tpp) cc_final: 0.5516 (tpp)
  outliers start: 37
  outliers final: 26
  residues processed: 208
  average time/residue: 0.1137
  time to fit residues: 35.4225
Evaluate side-chains
  194 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 166
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ASN
Chi-restraints excluded: chain A residue   79 LYS
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  403 CYS
Chi-restraints excluded: chain A residue  480 ASP
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  540 MET
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  610 SER
Chi-restraints excluded: chain A residue  711 MET
Chi-restraints excluded: chain A residue  753 ASP
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain B residue   17 ASP
Chi-restraints excluded: chain B residue   67 ILE
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  251 ASP
Chi-restraints excluded: chain C residue  394 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0870
   chunk 78 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 100 optimal weight:    9.9990
   chunk 109 optimal weight:    7.9990
   chunk 125 optimal weight:    0.0040
   chunk 142 optimal weight:    5.9990
   chunk 84 optimal weight:    6.9990
   chunk 129 optimal weight:    0.9980
   chunk 117 optimal weight:    0.9990
   overall best weight:    1.0174

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 899 ASN
B  59 ASN
B 133 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.227233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.184408 restraints weight = 16022.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.4092 rms_B_bonded: 3.77
r_work: 0.3479 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.3769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14318  Z= 0.138
  Angle     :  0.528   8.843  19468  Z= 0.286
  Chirality :  0.043   0.153   2155
  Planarity :  0.004   0.062   2376
  Dihedral  : 13.910 136.851   2136
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 10.36 %
    Favored  : 87.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.21), residues: 1631
  helix:  0.90 (0.22), residues: 558
  sheet:  0.03 (0.28), residues: 340
  loop : -0.63 (0.23), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 167 
 TYR   0.021   0.001   TYR A 554 
 PHE   0.015   0.001   PHE A 838 
 TRP   0.009   0.001   TRP A 470 
 HIS   0.005   0.001   HIS A 839 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.14 (14318)
  covalent geometry    : angle       0.52842 /  0.29 (19468)
  hydrogen bonds       : bond        0.04743 /  3.22 (  612)
  hydrogen bonds       : angle       4.49812 /  3.16 ( 1714)

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

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

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 172
  time to evaluate  : 0.508 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 ASP cc_start: 0.7514 (m-30) cc_final: 0.7050 (t70)
REVERT: A  131 TYR cc_start: 0.7378 (m-80) cc_final: 0.7052 (m-80)
REVERT: A  147 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7349 (t0)
REVERT: A  313 MET cc_start: 0.6883 (mmt) cc_final: 0.6092 (mmt)
REVERT: A  387 LYS cc_start: 0.7303 (ttpp) cc_final: 0.6932 (ttpt)
REVERT: A  404 LYS cc_start: 0.8498 (tttt) cc_final: 0.8067 (tmtt)
REVERT: A  462 ASP cc_start: 0.8170 (m-30) cc_final: 0.7946 (m-30)
REVERT: A  709 ASN cc_start: 0.8243 (p0) cc_final: 0.7927 (p0)
REVERT: A  725 ASP cc_start: 0.6663 (t0) cc_final: 0.5971 (p0)
REVERT: A  819 SER cc_start: 0.8632 (m) cc_final: 0.8376 (t)
REVERT: A  996 MET cc_start: 0.7500 (tpt) cc_final: 0.7010 (tpp)
REVERT: B  126 LYS cc_start: 0.8219 (ttmt) cc_final: 0.7716 (tptp)
REVERT: C   32 ASN cc_start: 0.6302 (m-40) cc_final: 0.5928 (m-40)
REVERT: C   95 MET cc_start: 0.6278 (tpp) cc_final: 0.5904 (tpp)
REVERT: C  118 LEU cc_start: 0.2619 (OUTLIER) cc_final: 0.2381 (mp)
REVERT: C  184 MET cc_start: 0.5791 (tpp) cc_final: 0.5451 (tpp)
  outliers start: 33
  outliers final: 25
  residues processed: 194
  average time/residue: 0.1200
  time to fit residues: 34.5490
Evaluate side-chains
  184 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 157
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ASN
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   79 LYS
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  403 CYS
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  480 ASP
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  540 MET
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  610 SER
Chi-restraints excluded: chain A residue  711 MET
Chi-restraints excluded: chain A residue  753 ASP
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain B residue   17 ASP
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  251 ASP
Chi-restraints excluded: chain C residue  394 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9980
   chunk 83 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0070
   chunk 18 optimal weight:    0.9990
   chunk 138 optimal weight:   40.0000
   chunk 82 optimal weight:    1.9990
   overall best weight:    1.2004

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 185 HIS
A 899 ASN
** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.224705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.169442 restraints weight = 15968.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3935 rms_B_bonded: 1.91
r_work: 0.3633 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3490 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.4033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14318  Z= 0.148
  Angle     :  0.536   8.410  19468  Z= 0.290
  Chirality :  0.044   0.176   2155
  Planarity :  0.004   0.060   2376
  Dihedral  : 13.909 138.896   2136
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 10.50 %
    Favored  : 86.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.21), residues: 1631
  helix:  0.85 (0.22), residues: 559
  sheet: -0.08 (0.27), residues: 351
  loop : -0.70 (0.23), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 197 
 TYR   0.023   0.002   TYR A 554 
 PHE   0.019   0.002   PHE A   9 
 TRP   0.009   0.001   TRP A 470 
 HIS   0.005   0.001   HIS A 839 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.15 (14318)
  covalent geometry    : angle       0.53614 /  0.29 (19468)
  hydrogen bonds       : bond        0.04742 /  3.22 (  612)
  hydrogen bonds       : angle       4.46511 /  3.13 ( 1714)

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

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

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 169
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 ASP cc_start: 0.7552 (m-30) cc_final: 0.7120 (t70)
REVERT: A   88 MET cc_start: 0.7392 (mmm) cc_final: 0.7099 (mmm)
REVERT: A  131 TYR cc_start: 0.7461 (m-80) cc_final: 0.7163 (m-80)
REVERT: A  147 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7481 (t0)
REVERT: A  313 MET cc_start: 0.7070 (mmt) cc_final: 0.6299 (mmt)
REVERT: A  404 LYS cc_start: 0.8452 (tttt) cc_final: 0.8051 (tmtt)
REVERT: A  709 ASN cc_start: 0.8271 (p0) cc_final: 0.8049 (p0)
REVERT: A  725 ASP cc_start: 0.6747 (t0) cc_final: 0.5911 (p0)
REVERT: A  819 SER cc_start: 0.8610 (m) cc_final: 0.8373 (t)
REVERT: A  834 ASP cc_start: 0.7416 (t0) cc_final: 0.7134 (p0)
REVERT: A  842 MET cc_start: 0.7803 (mpp) cc_final: 0.7564 (mmt)
REVERT: A  996 MET cc_start: 0.7301 (tpt) cc_final: 0.6849 (tpp)
REVERT: B  114 ASP cc_start: 0.8127 (m-30) cc_final: 0.7875 (m-30)
REVERT: B  126 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7813 (tptp)
REVERT: C   32 ASN cc_start: 0.6224 (m-40) cc_final: 0.5899 (m-40)
REVERT: C   95 MET cc_start: 0.6170 (tpp) cc_final: 0.5737 (tpp)
REVERT: C  118 LEU cc_start: 0.2612 (OUTLIER) cc_final: 0.2359 (mp)
REVERT: C  184 MET cc_start: 0.5749 (tpp) cc_final: 0.5490 (tpp)
  outliers start: 39
  outliers final: 29
  residues processed: 198
  average time/residue: 0.1114
  time to fit residues: 33.4284
Evaluate side-chains
  186 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 155
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ASN
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   79 LYS
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  403 CYS
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  480 ASP
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  540 MET
Chi-restraints excluded: chain A residue  610 SER
Chi-restraints excluded: chain A residue  753 ASP
Chi-restraints excluded: chain A residue  899 ASN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain B residue   17 ASP
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   97 GLU
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  251 ASP
Chi-restraints excluded: chain C residue  394 CYS
Chi-restraints excluded: chain C residue  408 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 119 optimal weight:   10.0000
   chunk 142 optimal weight:   50.0000
   chunk 93 optimal weight:    8.9990
   chunk 50 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0670
   chunk 92 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 130 optimal weight:    0.0370
   chunk 71 optimal weight:    0.9990
   chunk 109 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.5396

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.226433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.172536 restraints weight = 16026.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3967 rms_B_bonded: 2.03
r_work: 0.3646 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3501 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.4133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  14318  Z= 0.110
  Angle     :  0.510   7.847  19468  Z= 0.275
  Chirality :  0.042   0.255   2155
  Planarity :  0.004   0.065   2376
  Dihedral  : 13.787 138.054   2136
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 11.49 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.21), residues: 1631
  helix:  1.01 (0.22), residues: 559
  sheet: -0.11 (0.27), residues: 350
  loop : -0.70 (0.23), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 674 
 TYR   0.012   0.001   TYR A 300 
 PHE   0.013   0.001   PHE A   9 
 TRP   0.010   0.001   TRP A 470 
 HIS   0.005   0.001   HIS A 839 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00226 /  0.11 (14318)
  covalent geometry    : angle       0.51048 /  0.28 (19468)
  hydrogen bonds       : bond        0.04232 /  2.88 (  612)
  hydrogen bonds       : angle       4.40388 /  3.10 ( 1714)

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

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

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 168
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 ASP cc_start: 0.7578 (m-30) cc_final: 0.7145 (t70)
REVERT: A  131 TYR cc_start: 0.7420 (m-80) cc_final: 0.7046 (m-80)
REVERT: A  147 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7472 (t0)
REVERT: A  313 MET cc_start: 0.7056 (mmt) cc_final: 0.6286 (mmt)
REVERT: A  404 LYS cc_start: 0.8461 (tttt) cc_final: 0.8041 (tmtt)
REVERT: A  485 THR cc_start: 0.8442 (m) cc_final: 0.8170 (m)
REVERT: A  709 ASN cc_start: 0.8239 (p0) cc_final: 0.8023 (p0)
REVERT: A  725 ASP cc_start: 0.6778 (t0) cc_final: 0.5941 (p0)
REVERT: A  819 SER cc_start: 0.8557 (m) cc_final: 0.8301 (t)
REVERT: A  834 ASP cc_start: 0.7360 (t0) cc_final: 0.7102 (p0)
REVERT: A  842 MET cc_start: 0.7696 (mpp) cc_final: 0.7480 (mmt)
REVERT: A  996 MET cc_start: 0.7104 (tpt) cc_final: 0.6674 (tpp)
REVERT: B  126 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7779 (tptp)
REVERT: C   32 ASN cc_start: 0.6353 (m-40) cc_final: 0.6076 (m-40)
REVERT: C   95 MET cc_start: 0.6210 (tpp) cc_final: 0.5729 (tpp)
REVERT: C  118 LEU cc_start: 0.2629 (OUTLIER) cc_final: 0.2369 (mp)
REVERT: C  184 MET cc_start: 0.5761 (tpp) cc_final: 0.5501 (tpp)
  outliers start: 33
  outliers final: 24
  residues processed: 191
  average time/residue: 0.1173
  time to fit residues: 33.4370
Evaluate side-chains
  188 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 162
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ASN
Chi-restraints excluded: chain A residue   79 LYS
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  403 CYS
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  480 ASP
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  540 MET
Chi-restraints excluded: chain A residue  610 SER
Chi-restraints excluded: chain A residue  753 ASP
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain B residue   17 ASP
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  251 ASP
Chi-restraints excluded: chain C residue  394 CYS
Chi-restraints excluded: chain C residue  408 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 113 optimal weight:    3.9990
   chunk 87 optimal weight:   20.0000
   chunk 67 optimal weight:    0.0050
   chunk 89 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 143 optimal weight:    1.9990
   chunk 131 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 112 optimal weight:    0.5980
   overall best weight:    1.1200

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 899 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.224878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.179968 restraints weight = 15873.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.4054 rms_B_bonded: 3.89
r_work: 0.3456 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.4290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14318  Z= 0.143
  Angle     :  0.531   8.349  19468  Z= 0.285
  Chirality :  0.043   0.192   2155
  Planarity :  0.004   0.059   2376
  Dihedral  : 13.812 139.285   2136
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 11.75 %
    Favored  : 86.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.21), residues: 1631
  helix:  0.96 (0.22), residues: 564
  sheet: -0.09 (0.27), residues: 348
  loop : -0.74 (0.23), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 674 
 TYR   0.015   0.001   TYR A 554 
 PHE   0.014   0.001   PHE A   9 
 TRP   0.021   0.002   TRP C  43 
 HIS   0.007   0.001   HIS A 185 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.14 (14318)
  covalent geometry    : angle       0.53123 /  0.29 (19468)
  hydrogen bonds       : bond        0.04464 /  3.04 (  612)
  hydrogen bonds       : angle       4.40563 /  3.09 ( 1714)

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

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

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 169
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 ASP cc_start: 0.7590 (m-30) cc_final: 0.7158 (t70)
REVERT: A   88 MET cc_start: 0.7461 (mmm) cc_final: 0.7243 (mmm)
REVERT: A  131 TYR cc_start: 0.7481 (m-80) cc_final: 0.7063 (m-80)
REVERT: A  147 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7532 (t0)
REVERT: A  313 MET cc_start: 0.7035 (mmt) cc_final: 0.6280 (mmt)
REVERT: A  485 THR cc_start: 0.8486 (m) cc_final: 0.8276 (m)
REVERT: A  709 ASN cc_start: 0.8301 (p0) cc_final: 0.8059 (p0)
REVERT: A  725 ASP cc_start: 0.6924 (t0) cc_final: 0.5886 (p0)
REVERT: A  834 ASP cc_start: 0.7440 (t0) cc_final: 0.7142 (p0)
REVERT: A  842 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7408 (mmt)
REVERT: A  996 MET cc_start: 0.7121 (tpt) cc_final: 0.6781 (tpt)
REVERT: B  126 LYS cc_start: 0.8333 (ttmt) cc_final: 0.7827 (tptp)
REVERT: C   32 ASN cc_start: 0.6119 (m-40) cc_final: 0.5861 (m-40)
REVERT: C   87 PHE cc_start: 0.5547 (m-80) cc_final: 0.5176 (m-80)
REVERT: C   95 MET cc_start: 0.6356 (tpp) cc_final: 0.5802 (tpp)
REVERT: C  118 LEU cc_start: 0.2568 (OUTLIER) cc_final: 0.2310 (mp)
REVERT: C  184 MET cc_start: 0.5765 (tpp) cc_final: 0.5506 (tpp)
  outliers start: 33
  outliers final: 25
  residues processed: 193
  average time/residue: 0.1068
  time to fit residues: 31.9257
Evaluate side-chains
  185 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 157
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ASN
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   79 LYS
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  403 CYS
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  480 ASP
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  540 MET
Chi-restraints excluded: chain A residue  610 SER
Chi-restraints excluded: chain A residue  753 ASP
Chi-restraints excluded: chain A residue  842 MET
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain B residue   17 ASP
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  394 CYS
Chi-restraints excluded: chain C residue  408 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 91 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 116 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 100 optimal weight:    9.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 899 ASN
C 134 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.223838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.169661 restraints weight = 16017.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 2.05
r_work: 0.3599 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3456 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.4415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14318  Z= 0.151
  Angle     :  0.552  12.630  19468  Z= 0.293
  Chirality :  0.043   0.172   2155
  Planarity :  0.004   0.058   2376
  Dihedral  : 13.868 139.878   2136
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 12.21 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.21), residues: 1631
  helix:  0.95 (0.22), residues: 565
  sheet: -0.12 (0.28), residues: 336
  loop : -0.79 (0.23), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 674 
 TYR   0.015   0.001   TYR A 554 
 PHE   0.014   0.001   PHE A 838 
 TRP   0.013   0.001   TRP C  43 
 HIS   0.007   0.001   HIS A 185 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.15 (14318)
  covalent geometry    : angle       0.55157 /  0.29 (19468)
  hydrogen bonds       : bond        0.04536 /  3.08 (  612)
  hydrogen bonds       : angle       4.40780 /  3.09 ( 1714)

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

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

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 164
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 ASP cc_start: 0.7550 (m-30) cc_final: 0.7109 (t70)
REVERT: A   88 MET cc_start: 0.7457 (mmm) cc_final: 0.7226 (mmm)
REVERT: A  131 TYR cc_start: 0.7530 (m-80) cc_final: 0.7143 (m-80)
REVERT: A  147 ASN cc_start: 0.8156 (OUTLIER) cc_final: 0.7578 (t0)
REVERT: A  709 ASN cc_start: 0.8289 (p0) cc_final: 0.8043 (p0)
REVERT: A  725 ASP cc_start: 0.7026 (t0) cc_final: 0.6000 (p0)
REVERT: A  842 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7526 (mmt)
REVERT: A  996 MET cc_start: 0.7077 (tpt) cc_final: 0.6702 (tpp)
REVERT: B  126 LYS cc_start: 0.8249 (ttmt) cc_final: 0.7813 (tptp)
REVERT: B  167 ARG cc_start: 0.7486 (mmt180) cc_final: 0.6889 (mmm160)
REVERT: C   32 ASN cc_start: 0.6245 (m-40) cc_final: 0.5943 (m-40)
REVERT: C   95 MET cc_start: 0.6393 (tpp) cc_final: 0.6002 (tpp)
REVERT: C  118 LEU cc_start: 0.2565 (OUTLIER) cc_final: 0.2308 (mp)
REVERT: C  184 MET cc_start: 0.5835 (tpp) cc_final: 0.5589 (tpp)
  outliers start: 34
  outliers final: 27
  residues processed: 188
  average time/residue: 0.1175
  time to fit residues: 33.3855
Evaluate side-chains
  187 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 157
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ASN
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   79 LYS
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  403 CYS
Chi-restraints excluded: chain A residue  480 ASP
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  540 MET
Chi-restraints excluded: chain A residue  610 SER
Chi-restraints excluded: chain A residue  753 ASP
Chi-restraints excluded: chain A residue  842 MET
Chi-restraints excluded: chain A residue  899 ASN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain B residue   17 ASP
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  251 ASP
Chi-restraints excluded: chain C residue  394 CYS
Chi-restraints excluded: chain C residue  408 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 88 optimal weight:    0.0050
   chunk 20 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 119 optimal weight:   10.0000
   chunk 80 optimal weight:    4.9990
   chunk 32 optimal weight:    0.5980
   chunk 81 optimal weight:    3.9990
   chunk 143 optimal weight:   20.0000
   chunk 33 optimal weight:    1.9990
   chunk 31 optimal weight:    0.1980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.4996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 899 ASN
B  55 GLN
B 111 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.225718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.171137 restraints weight = 15973.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3957 rms_B_bonded: 2.14
r_work: 0.3621 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3477 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.4472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  14318  Z= 0.111
  Angle     :  0.519  10.882  19468  Z= 0.278
  Chirality :  0.042   0.162   2155
  Planarity :  0.004   0.056   2376
  Dihedral  : 13.738 138.836   2136
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 12.34 %
    Favored  : 85.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.21), residues: 1631
  helix:  1.12 (0.22), residues: 564
  sheet: -0.04 (0.27), residues: 349
  loop : -0.74 (0.23), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 674 
 TYR   0.016   0.001   TYR A 900 
 PHE   0.019   0.001   PHE C  87 
 TRP   0.027   0.002   TRP C 136 
 HIS   0.005   0.001   HIS A 897 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00230 /  0.11 (14318)
  covalent geometry    : angle       0.51884 /  0.28 (19468)
  hydrogen bonds       : bond        0.04041 /  2.75 (  612)
  hydrogen bonds       : angle       4.34192 /  3.05 ( 1714)

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

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

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3262 Ramachandran restraints generated.
    1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 160
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 ASP cc_start: 0.7585 (m-30) cc_final: 0.7148 (t70)
REVERT: A   88 MET cc_start: 0.7455 (mmm) cc_final: 0.7202 (mmm)
REVERT: A  131 TYR cc_start: 0.7494 (m-80) cc_final: 0.7117 (m-80)
REVERT: A  147 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7580 (t0)
REVERT: A  709 ASN cc_start: 0.8277 (p0) cc_final: 0.8024 (p0)
REVERT: A  725 ASP cc_start: 0.7016 (t0) cc_final: 0.6060 (p0)
REVERT: A  842 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7479 (mmt)
REVERT: A  996 MET cc_start: 0.7096 (tpt) cc_final: 0.6713 (tpp)
REVERT: B  126 LYS cc_start: 0.8273 (ttmt) cc_final: 0.7812 (tptp)
REVERT: B  167 ARG cc_start: 0.7455 (mmt180) cc_final: 0.6905 (mmm160)
REVERT: C   32 ASN cc_start: 0.6194 (m-40) cc_final: 0.5922 (m-40)
REVERT: C   95 MET cc_start: 0.6543 (tpp) cc_final: 0.6043 (tpp)
REVERT: C  118 LEU cc_start: 0.2652 (OUTLIER) cc_final: 0.2383 (mp)
REVERT: C  184 MET cc_start: 0.5824 (tpp) cc_final: 0.5585 (tpp)
  outliers start: 29
  outliers final: 23
  residues processed: 179
  average time/residue: 0.1128
  time to fit residues: 30.8891
Evaluate side-chains
  181 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 155
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ASN
Chi-restraints excluded: chain A residue   79 LYS
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  403 CYS
Chi-restraints excluded: chain A residue  480 ASP
Chi-restraints excluded: chain A residue  512 GLU
Chi-restraints excluded: chain A residue  540 MET
Chi-restraints excluded: chain A residue  610 SER
Chi-restraints excluded: chain A residue  812 SER
Chi-restraints excluded: chain A residue  842 MET
Chi-restraints excluded: chain A residue  899 ASN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain B residue   17 ASP
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  223 ILE
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  251 ASP
Chi-restraints excluded: chain C residue  394 CYS
Chi-restraints excluded: chain C residue  408 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 95 optimal weight:    7.9990
   chunk 134 optimal weight:    4.9990
   chunk 150 optimal weight:    7.9990
   chunk 121 optimal weight:    6.9990
   chunk 56 optimal weight:    0.0370
   chunk 118 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 120 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 138 optimal weight:    2.9990
   overall best weight:    1.2062

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 899 ASN
B 109 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.224053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.178989 restraints weight = 15939.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.4048 rms_B_bonded: 3.91
r_work: 0.3452 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.4535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14318  Z= 0.145
  Angle     :  0.539  10.725  19468  Z= 0.287
  Chirality :  0.043   0.159   2155
  Planarity :  0.004   0.056   2376
  Dihedral  : 13.776 139.682   2136
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 12.87 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.21), residues: 1631
  helix:  1.02 (0.22), residues: 564
  sheet:  0.01 (0.28), residues: 337
  loop : -0.78 (0.23), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 674 
 TYR   0.019   0.001   TYR A 900 
 PHE   0.014   0.001   PHE C  87 
 TRP   0.022   0.002   TRP C 136 
 HIS   0.007   0.001   HIS A 185 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.15 (14318)
  covalent geometry    : angle       0.53940 /  0.29 (19468)
  hydrogen bonds       : bond        0.04337 /  2.95 (  612)
  hydrogen bonds       : angle       4.37136 /  3.06 ( 1714)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4123.16 seconds
wall clock time: 71 minutes 18.17 seconds (4278.17 seconds total)