Starting phenix.real_space_refine
on Sat Aug 23 11:44:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hdz_34684/08_2025/8hdz_34684.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hdz_34684/08_2025/8hdz_34684.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hdz_34684/08_2025/8hdz_34684.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hdz_34684/08_2025/8hdz_34684.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hdz_34684/08_2025/8hdz_34684.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hdz_34684/08_2025/8hdz_34684.map"
  }
  resolution = 3.05
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      62      5.16       5
     C    7619      2.51       5
     N    1951      2.21       5
     O    2229      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11861
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 813, 6622
          Classifications: {'peptide': 813}
          Link IDs: {'PTRANS': 30, 'TRANS': 782}
    Chain: "C"
      Number of atoms: 3467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3467
          Classifications: {'peptide': 426}
          Link IDs: {'PTRANS': 10, 'TRANS': 415}
    Chain: "B"
      Number of atoms: 1772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1772
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 13, 'TRANS': 204}
  Time building chain proxies: 2.91, per 1000 atoms: 0.25
  Number of scatterers: 11861
  At special positions: 0
  Unit cell: (92.4, 124.32, 141.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      62     16.00
     O    2229      8.00
     N    1951      7.00
     C    7619      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: 0.94
  Conformation dependent library (CDL) restraints added in 549.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2782

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 17 sheets defined
      36.5% alpha, 17.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 108 through 117
      removed outlier: 3.670A  pdb=" N   ASN A 117 " --> pdb=" O   PHE A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 149
    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 220
    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 281
    Processing helix  chain 'A' and resid 331 through 339
    Processing helix  chain 'A' and resid 345 through 354
      removed outlier: 3.830A  pdb=" N   PHE A 354 " --> pdb=" O   SER A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 391
      removed outlier: 3.939A  pdb=" N   THR A 384 " --> pdb=" O   GLY A 380 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   THR A 391 " --> pdb=" O   LYS A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 445
    Processing helix  chain 'A' and resid 448 through 473
      removed outlier: 3.668A  pdb=" N   CYS A 466 " --> pdb=" O   ASP A 462 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   GLN A 467 " --> pdb=" O   ALA A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 487
    Processing helix  chain 'A' and resid 497 through 514
      removed outlier: 3.872A  pdb=" N   GLY A 504 " --> pdb=" O   THR A 500 " (cutoff:3.500A)
      Proline residue:  A 505  - end of helix
    Processing helix  chain 'A' and resid 552 through 562
    Processing helix  chain 'A' and resid 576 through 591
      removed outlier: 3.787A  pdb=" N   GLN A 589 " --> pdb=" O   GLN A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 642
    Processing helix  chain 'A' and resid 646 through 665
    Processing helix  chain 'A' and resid 666 through 672
      removed outlier: 3.880A  pdb=" N   GLY A 672 " --> pdb=" O   TYR A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 703
    Processing helix  chain 'A' and resid 763 through 781
    Processing helix  chain 'C' and resid 8 through 11
    Processing helix  chain 'C' and resid 12 through 19
      removed outlier: 3.881A  pdb=" N   LYS C  18 " --> pdb=" O   LEU C  14 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 37
      removed outlier: 4.484A  pdb=" N   LYS C  30 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 59
    Processing helix  chain 'C' and resid 107 through 121
    Processing helix  chain 'C' and resid 132 through 135
    Processing helix  chain 'C' and resid 147 through 159
      removed outlier: 3.661A  pdb=" N   ILE C 151 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   TYR C 158 " --> pdb=" O   LEU C 154 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLY C 159 " --> pdb=" O   ALA C 155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 177 through 188
    Processing helix  chain 'C' and resid 249 through 257
      removed outlier: 4.123A  pdb=" N   LYS C 257 " --> pdb=" O   LEU C 253 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 285 through 298
      removed outlier: 3.570A  pdb=" N   VAL C 289 " --> pdb=" O   THR C 285 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   THR C 296 " --> pdb=" O   ARG C 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 316 through 323
      removed outlier: 3.621A  pdb=" N   THR C 320 " --> pdb=" O   LEU C 316 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 330 through 341
    Processing helix  chain 'C' and resid 341 through 350
      removed outlier: 3.565A  pdb=" N   LYS C 349 " --> pdb=" O   LYS C 345 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ASN C 350 " --> pdb=" O   ARG C 346 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 352 through 361
    Processing helix  chain 'C' and resid 367 through 374
      removed outlier: 3.538A  pdb=" N   ASN C 374 " --> pdb=" O   THR C 370 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 392 through 396
      removed outlier: 3.992A  pdb=" N   ASN C 396 " --> pdb=" O   ASN C 393 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 397 through 406
      removed outlier: 3.574A  pdb=" N   GLU C 401 " --> pdb=" O   ASN C 397 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 425
    Processing helix  chain 'B' and resid 16 through 18
      No H-bonds generated for 'chain 'B' and resid 16 through 18'
    Processing helix  chain 'B' and resid 19 through 32
      removed outlier: 4.212A  pdb=" N   SER B  24 " --> pdb=" O   GLU B  20 " (cutoff:3.500A)
      removed outlier: 4.987A  pdb=" N   GLN B  25 " --> pdb=" O   PRO B  21 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLU B  32 " --> pdb=" O   GLU B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 50
      removed outlier: 3.664A  pdb=" N   PHE B  50 " --> pdb=" O   ASP B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 101
      removed outlier: 3.647A  pdb=" N   LYS B  90 " --> pdb=" O   LYS B  86 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   ILE B  96 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ARG B  98 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   LEU B  99 " --> pdb=" O   SER B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 150
      removed outlier: 3.828A  pdb=" N   LEU B 145 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 170
    Processing helix  chain 'B' and resid 194 through 205
    Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126
      removed outlier: 5.604A  pdb=" N   CYS A   5 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   ARG A  23 " --> pdb=" O   CYS A   5 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ASN A   7 " --> pdb=" O   LYS A  21 " (cutoff:3.500A)
      removed outlier: 8.170A  pdb=" N   TYR A 140 " --> pdb=" O   THR A  29 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   PHE A  31 " --> pdb=" O   TYR A 140 " (cutoff:3.500A)
      removed outlier: 6.954A  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: 6.070A  pdb=" N   LEU A  90 " --> pdb=" O   PRO A  59 " (cutoff:3.500A)
      removed outlier: 7.682A  pdb=" N   GLU A  92 " --> pdb=" O   ALA A  57 " (cutoff:3.500A)
      removed outlier: 6.436A  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: 6.654A  pdb=" N   SER A  73 " --> pdb=" O   VAL A 573 " (cutoff:3.500A)
      removed outlier: 5.851A  pdb=" N   LEU A 568 " --> pdb=" O   ASP A 616 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ASP A 616 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLY A 570 " --> pdb=" O   ILE A 614 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   SER A 610 " --> pdb=" O   SER A 574 " (cutoff:3.500A)
      removed outlier: 3.700A  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: 6.133A  pdb=" N   LEU A 222 " --> pdb=" O   LEU A 238 " (cutoff:3.500A)
      removed outlier: 7.960A  pdb=" N   VAL A 237 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   THR A 201 " --> pdb=" O   VAL A 237 " (cutoff:3.500A)
      removed outlier: 7.401A  pdb=" N   CYS A 239 " --> pdb=" O   THR A 201 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   ILE A 203 " --> pdb=" O   CYS A 239 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   SER A 184 " --> pdb=" O   ASN A 204 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU A 165 " --> pdb=" O   VAL A 260 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 286 through 287
    Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 302
    Processing sheet with id=AA7, first strand: chain 'A' and resid 408 through 411
      removed outlier: 3.825A  pdb=" N   LEU A 411 " --> pdb=" O   GLY A 414 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   VAL A 417 " --> pdb=" O   PHE A 370 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 394 through 397
    Processing sheet with id=AA9, first strand: chain 'A' and resid 732 through 734
      removed outlier: 3.510A  pdb=" N   ARG A 713 " --> pdb=" O   GLU A 706 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLU A 706 " --> pdb=" O   ARG A 713 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   SER A 747 " --> pdb=" O   GLU A 758 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   GLU A 758 " --> pdb=" O   SER A 747 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   TYR A 749 " --> pdb=" O   PHE A 756 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL A 755 " --> pdb=" O   PHE A 548 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   PHE A 548 " --> pdb=" O   VAL A 755 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE A 547 " --> pdb=" O   ALA A 793 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   ALA A 793 " --> pdb=" O   ILE A 547 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   ASP A 549 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 5.712A  pdb=" N   PHE A 791 " --> pdb=" O   ASP A 549 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   TYR A 795 " --> pdb=" O   TYR A 811 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   TYR A 811 " --> pdb=" O   TYR A 795 " (cutoff:3.500A)
      removed outlier: 5.673A  pdb=" N   ASN A 797 " --> pdb=" O   MET A 809 " (cutoff:3.500A)
      removed outlier: 5.225A  pdb=" N   MET A 809 " --> pdb=" O   ASN A 797 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   LYS A 805 " --> pdb=" O   GLN A 801 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 61 through 65
      removed outlier: 5.969A  pdb=" N   ARG C 207 " --> pdb=" O   TYR C  61 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   GLU C  63 " --> pdb=" O   ARG C 207 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 69 through 70
      removed outlier: 3.516A  pdb=" N   PHE C  69 " --> pdb=" O   PHE C 176 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 166 through 170
    Processing sheet with id=AB4, first strand: chain 'C' and resid 86 through 87
      removed outlier: 4.023A  pdb=" N   PHE C 126 " --> pdb=" O   ILE C 142 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ARG C 128 " --> pdb=" O   ASP C 140 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   ASP C 140 " --> pdb=" O   ARG C 128 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   VAL C 130 " --> pdb=" O   MET C 138 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   MET C 138 " --> pdb=" O   VAL C 130 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 220 through 223
      removed outlier: 5.352A  pdb=" N   ILE C 238 " --> pdb=" O   GLU C 221 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 267 through 268
      removed outlier: 3.597A  pdb=" N   LYS C 267 " --> pdb=" O   ILE C 274 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 375 through 380
      removed outlier: 5.996A  pdb=" N   GLU C 380 " --> pdb=" O   VAL C 384 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   VAL C 384 " --> pdb=" O   GLU C 380 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 116 through 120
      removed outlier: 5.731A  pdb=" N   CYS B  63 " --> pdb=" O   TYR B 156 " (cutoff:3.500A)
      removed outlier: 7.473A  pdb=" N   LEU B 158 " --> pdb=" O   CYS B  63 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   CYS B  65 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   LEU B 155 " --> pdb=" O   ILE B 177 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   GLY B 179 " --> pdb=" O   LEU B 155 " (cutoff:3.500A)
      removed outlier: 5.607A  pdb=" N   CYS B 157 " --> pdb=" O   GLY B 179 " (cutoff:3.500A)

    443 hydrogen bonds defined for protein.
    1269 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.55

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3780
        1.34 -     1.46: 2569
        1.46 -     1.58: 5678
        1.58 -     1.69: 0
        1.69 -     1.81: 93
  Bond restraints: 12120
  Sorted by residual:
  bond pdb=" C   GLU A  93 "
       pdb=" O   GLU A  93 "
    ideal  model  delta    sigma   weight residual
    1.238  1.249 -0.011 1.28e-02 6.10e+03 7.83e-01
  bond pdb=" C   PRO A 593 "
       pdb=" N   PRO A 594 "
    ideal  model  delta    sigma   weight residual
    1.335  1.345 -0.010 1.28e-02 6.10e+03 6.19e-01
  bond pdb=" CA  ILE A 153 "
       pdb=" CB  ILE A 153 "
    ideal  model  delta    sigma   weight residual
    1.537  1.547 -0.010 1.29e-02 6.01e+03 6.11e-01
  bond pdb=" CA  LEU C  10 "
       pdb=" CB  LEU C  10 "
    ideal  model  delta    sigma   weight residual
    1.533  1.545 -0.012 1.66e-02 3.63e+03 5.28e-01
  bond pdb=" CB  PRO B  82 "
       pdb=" CG  PRO B  82 "
    ideal  model  delta    sigma   weight residual
    1.492  1.525 -0.033 5.00e-02 4.00e+02 4.31e-01
  ... (remaining 12115 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 16281
        2.13 -     4.26: 94
        4.26 -     6.39: 9
        6.39 -     8.51: 2
        8.51 -    10.64: 1
  Bond angle restraints: 16387
  Sorted by residual:
  angle pdb=" CA  LEU C  10 "
        pdb=" CB  LEU C  10 "
        pdb=" CG  LEU C  10 "
      ideal   model   delta    sigma   weight residual
     116.30  126.94  -10.64 3.50e+00 8.16e-02 9.25e+00
  angle pdb=" CA  LEU C 202 "
        pdb=" CB  LEU C 202 "
        pdb=" CG  LEU C 202 "
      ideal   model   delta    sigma   weight residual
     116.30  124.50   -8.20 3.50e+00 8.16e-02 5.49e+00
  angle pdb=" C   GLU C  36 "
        pdb=" N   TRP C  37 "
        pdb=" CA  TRP C  37 "
      ideal   model   delta    sigma   weight residual
     122.62  118.74    3.88 1.78e+00 3.16e-01 4.76e+00
  angle pdb=" N   ILE A 180 "
        pdb=" CA  ILE A 180 "
        pdb=" C   ILE A 180 "
      ideal   model   delta    sigma   weight residual
     112.12  110.42    1.70 8.40e-01 1.42e+00 4.08e+00
  angle pdb=" CA  LEU A 517 "
        pdb=" CB  LEU A 517 "
        pdb=" CG  LEU A 517 "
      ideal   model   delta    sigma   weight residual
     116.30  123.33   -7.03 3.50e+00 8.16e-02 4.03e+00
  ... (remaining 16382 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.15: 6437
       16.15 -    32.29: 704
       32.29 -    48.44: 143
       48.44 -    64.58: 27
       64.58 -    80.73: 9
  Dihedral angle restraints: 7320
    sinusoidal: 3002
      harmonic: 4318
  Sorted by residual:
  dihedral pdb=" CA  TYR B  70 "
           pdb=" C   TYR B  70 "
           pdb=" N   PRO B  71 "
           pdb=" CA  PRO B  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.76  -17.24     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CA  ASP C 178 "
           pdb=" CB  ASP C 178 "
           pdb=" CG  ASP C 178 "
           pdb=" OD1 ASP C 178 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.04   59.04     1      2.00e+01 2.50e-03 1.17e+01
  dihedral pdb=" CA  ASP A 728 "
           pdb=" CB  ASP A 728 "
           pdb=" CG  ASP A 728 "
           pdb=" OD1 ASP A 728 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.00   59.00     1      2.00e+01 2.50e-03 1.16e+01
  ... (remaining 7317 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1098
       0.027 -    0.054: 417
       0.054 -    0.080: 160
       0.080 -    0.107: 95
       0.107 -    0.134: 47
  Chirality restraints: 1817
  Sorted by residual:
  chirality pdb=" CA  ILE A 158 "
            pdb=" N   ILE A 158 "
            pdb=" C   ILE A 158 "
            pdb=" CB  ILE A 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.47e-01
  chirality pdb=" CA  ILE A 516 "
            pdb=" N   ILE A 516 "
            pdb=" C   ILE A 516 "
            pdb=" CB  ILE A 516 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.09e-01
  chirality pdb=" CA  ILE C  77 "
            pdb=" N   ILE C  77 "
            pdb=" C   ILE C  77 "
            pdb=" CB  ILE C  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.06e-01
  ... (remaining 1814 not shown)

  Planarity restraints: 2085
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 592 "    0.032 5.00e-02 4.00e+02   4.93e-02 3.89e+00
        pdb=" N   PRO A 593 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 593 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 593 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B  45 "   -0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO B  46 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B  46 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B  46 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  43 "    0.025 5.00e-02 4.00e+02   3.69e-02 2.17e+00
        pdb=" N   PRO B  44 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B  44 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B  44 "    0.021 5.00e-02 4.00e+02
  ... (remaining 2082 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 407
        2.72 -     3.26: 11714
        3.26 -     3.81: 19147
        3.81 -     4.35: 23103
        4.35 -     4.90: 39529
  Nonbonded interactions: 93900
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 302 "
            pdb=" O   LEU C 361 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" OH  TYR A 190 "
            pdb=" OD2 ASP A 192 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   LYS C 310 "
            pdb=" NE2 GLN C 318 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" ND2 ASN C 304 "
            pdb=" O   GLY C 362 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" OG  SER A 564 "
            pdb=" OE1 GLU A 566 "
     model   vdw
     2.239 3.040
  ... (remaining 93895 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:             2.220
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     12.600
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4673
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12120  Z= 0.086
  Angle     :  0.437  10.643  16387  Z= 0.228
  Chirality :  0.040   0.134   1817
  Planarity :  0.003   0.049   2085
  Dihedral  : 13.939  80.731   4538
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.27 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.18 (0.23), residues: 1451
  helix:  1.26 (0.25), residues: 474
  sheet:  0.88 (0.34), residues: 258
  loop : -0.96 (0.24), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  23 
 TYR   0.013   0.001   TYR B  70 
 PHE   0.007   0.001   PHE A 200 
 TRP   0.023   0.001   TRP B 137 
 HIS   0.001   0.000   HIS A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00174 (12120)
  covalent geometry    : angle       0.43686 (16387)
  hydrogen bonds       : bond        0.14542 (  443)
  hydrogen bonds       : angle       6.32479 ( 1269)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
REVERT: A  168 GLU cc_start: 0.5299 (mm-30) cc_final: 0.4629 (tm-30)
REVERT: B  212 TRP cc_start: 0.3241 (m100) cc_final: 0.2938 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1231
  time to fit residues: 25.7932
Evaluate side-chains
  109 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 657 GLN
** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5391 r_free = 0.5391 target = 0.291966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4901 r_free = 0.4901 target = 0.228301 restraints weight = 12404.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.4850 rms_B_bonded: 2.65
r_work: 0.4559 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.4559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5587
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.086  12120  Z= 0.251
  Angle     :  0.734  13.391  16387  Z= 0.382
  Chirality :  0.049   0.176   1817
  Planarity :  0.006   0.054   2085
  Dihedral  :  4.865  22.430   1604
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.86 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 11.72 %
    Favored  : 86.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -0.65 (0.22), residues: 1451
  helix:  0.38 (0.24), residues: 463
  sheet:  0.48 (0.34), residues: 246
  loop : -1.28 (0.23), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 376 
 TYR   0.041   0.003   TYR A 190 
 PHE   0.022   0.002   PHE A  31 
 TRP   0.021   0.002   TRP C  37 
 HIS   0.009   0.002   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00582 (12120)
  covalent geometry    : angle       0.73358 (16387)
  hydrogen bonds       : bond        0.05643 (  443)
  hydrogen bonds       : angle       5.94826 ( 1269)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  335 ILE cc_start: 0.4953 (OUTLIER) cc_final: 0.4718 (mt)
REVERT: A  455 MET cc_start: 0.2819 (mtt) cc_final: 0.2595 (mtt)
REVERT: A  787 PHE cc_start: 0.5882 (m-80) cc_final: 0.5524 (m-80)
REVERT: C   95 MET cc_start: 0.3932 (tpp) cc_final: 0.3606 (tpp)
REVERT: C  138 MET cc_start: 0.4897 (tpp) cc_final: 0.4449 (tpp)
REVERT: B   23 MET cc_start: 0.3785 (tpp) cc_final: 0.3019 (ptt)
REVERT: B  206 ASN cc_start: 0.7814 (t0) cc_final: 0.7560 (p0)
  outliers start: 20
  outliers final: 14
  residues processed: 128
  average time/residue: 0.1133
  time to fit residues: 21.5292
Evaluate side-chains
  118 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 TYR
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  322 ASN
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  515 THR
Chi-restraints excluded: chain A residue  657 GLN
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 106 optimal weight:    7.9990
   chunk 9 optimal weight:    0.6980
   chunk 103 optimal weight:    8.9990
   chunk 81 optimal weight:    1.9990
   chunk 99 optimal weight:   20.0000
   chunk 1 optimal weight:    3.9990
   chunk 125 optimal weight:    0.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   8 HIS
B  31 ASN
B  52 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5423 r_free = 0.5423 target = 0.296365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.5159 r_free = 0.5159 target = 0.256808 restraints weight = 12514.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.5146 rms_B_bonded: 3.25
r_work: 0.4656 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.4656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5545
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12120  Z= 0.131
  Angle     :  0.544   9.599  16387  Z= 0.284
  Chirality :  0.043   0.175   1817
  Planarity :  0.004   0.053   2085
  Dihedral  :  4.278  19.791   1604
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.17 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 13.43 %
    Favored  : 85.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -0.38 (0.22), residues: 1451
  helix:  0.69 (0.24), residues: 471
  sheet:  0.74 (0.36), residues: 222
  loop : -1.19 (0.23), residues: 758

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 160 
 TYR   0.026   0.001   TYR A 190 
 PHE   0.011   0.001   PHE A  31 
 TRP   0.016   0.001   TRP C  37 
 HIS   0.009   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (12120)
  covalent geometry    : angle       0.54425 (16387)
  hydrogen bonds       : bond        0.04020 (  443)
  hydrogen bonds       : angle       5.36190 ( 1269)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 PHE cc_start: 0.6601 (OUTLIER) cc_final: 0.6255 (t80)
REVERT: A  787 PHE cc_start: 0.5410 (m-80) cc_final: 0.4821 (m-80)
REVERT: C   95 MET cc_start: 0.3906 (tpp) cc_final: 0.3630 (tpp)
REVERT: C  138 MET cc_start: 0.5029 (tpp) cc_final: 0.4712 (tpp)
REVERT: B   23 MET cc_start: 0.3733 (tpp) cc_final: 0.3307 (ppp)
  outliers start: 19
  outliers final: 11
  residues processed: 121
  average time/residue: 0.1109
  time to fit residues: 19.9720
Evaluate side-chains
  114 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  660 TYR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 93 optimal weight:    5.9990
   chunk 120 optimal weight:    0.5980
   chunk 133 optimal weight:    6.9990
   chunk 25 optimal weight:    0.5980
   chunk 54 optimal weight:    9.9990
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5429 r_free = 0.5429 target = 0.296978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.5159 r_free = 0.5159 target = 0.256800 restraints weight = 12434.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.5148 rms_B_bonded: 3.12
r_work: 0.4682 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.4682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5522
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12120  Z= 0.122
  Angle     :  0.533   8.866  16387  Z= 0.276
  Chirality :  0.043   0.183   1817
  Planarity :  0.004   0.053   2085
  Dihedral  :  4.103  19.050   1604
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.79 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 14.78 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -0.28 (0.23), residues: 1451
  helix:  0.83 (0.25), residues: 472
  sheet:  0.70 (0.36), residues: 224
  loop : -1.15 (0.23), residues: 755

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 497 
 TYR   0.027   0.001   TYR A 190 
 PHE   0.012   0.001   PHE C 410 
 TRP   0.016   0.001   TRP C  37 
 HIS   0.007   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (12120)
  covalent geometry    : angle       0.53268 (16387)
  hydrogen bonds       : bond        0.03616 (  443)
  hydrogen bonds       : angle       5.11324 ( 1269)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 PHE cc_start: 0.6537 (OUTLIER) cc_final: 0.6177 (t80)
REVERT: A  787 PHE cc_start: 0.5381 (m-80) cc_final: 0.4828 (m-80)
REVERT: C   95 MET cc_start: 0.3913 (tpp) cc_final: 0.3705 (tpp)
REVERT: C  138 MET cc_start: 0.5007 (tpp) cc_final: 0.4674 (tpp)
REVERT: B   23 MET cc_start: 0.3548 (tpp) cc_final: 0.3271 (ppp)
REVERT: B   29 PHE cc_start: 0.4826 (m-80) cc_final: 0.3650 (t80)
  outliers start: 25
  outliers final: 14
  residues processed: 128
  average time/residue: 0.1093
  time to fit residues: 21.0968
Evaluate side-chains
  120 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  701 VAL
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 91 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 105 optimal weight:   10.0000
   chunk 48 optimal weight:    0.0970
   chunk 77 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0870
   chunk 87 optimal weight:    0.0870
   chunk 117 optimal weight:    5.9990
   chunk 131 optimal weight:    2.9990
   overall best weight:    0.8536

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5430 r_free = 0.5430 target = 0.299051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5168 r_free = 0.5168 target = 0.260065 restraints weight = 12214.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.5151 rms_B_bonded: 3.01
r_work: 0.4689 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.4689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5518
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12120  Z= 0.123
  Angle     :  0.525   9.787  16387  Z= 0.271
  Chirality :  0.043   0.164   1817
  Planarity :  0.004   0.052   2085
  Dihedral  :  4.060  18.988   1604
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.17 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 14.93 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -0.24 (0.23), residues: 1451
  helix:  0.88 (0.25), residues: 471
  sheet:  0.66 (0.36), residues: 224
  loop : -1.10 (0.23), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 497 
 TYR   0.022   0.001   TYR A 190 
 PHE   0.015   0.001   PHE C 410 
 TRP   0.016   0.001   TRP C  37 
 HIS   0.006   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (12120)
  covalent geometry    : angle       0.52498 (16387)
  hydrogen bonds       : bond        0.03562 (  443)
  hydrogen bonds       : angle       5.05827 ( 1269)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 PHE cc_start: 0.6532 (OUTLIER) cc_final: 0.6080 (t80)
REVERT: A  724 MET cc_start: 0.5545 (mmm) cc_final: 0.5087 (mpp)
REVERT: A  787 PHE cc_start: 0.5339 (m-80) cc_final: 0.4796 (m-80)
REVERT: C   95 MET cc_start: 0.3961 (tpp) cc_final: 0.3673 (tpp)
REVERT: C  138 MET cc_start: 0.5070 (tpp) cc_final: 0.4652 (tpp)
REVERT: B   29 PHE cc_start: 0.5298 (m-80) cc_final: 0.3690 (t80)
REVERT: B  212 TRP cc_start: 0.3669 (m100) cc_final: 0.3265 (m100)
  outliers start: 32
  outliers final: 24
  residues processed: 135
  average time/residue: 0.1072
  time to fit residues: 21.6734
Evaluate side-chains
  132 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 107
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  322 ASN
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  701 VAL
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 121 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   chunk 135 optimal weight:    4.9990
   chunk 103 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   chunk 96 optimal weight:    6.9990
   chunk 105 optimal weight:    7.9990
   chunk 136 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9980
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 393 ASN
C 406 ASN
B 147 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5372 r_free = 0.5372 target = 0.289247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.4780 r_free = 0.4780 target = 0.215872 restraints weight = 12477.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.4707 rms_B_bonded: 3.01
r_work: 0.4499 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.4499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5671
moved from start:          0.3423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.089  12120  Z= 0.244
  Angle     :  0.714  14.338  16387  Z= 0.369
  Chirality :  0.048   0.246   1817
  Planarity :  0.005   0.056   2085
  Dihedral  :  4.950  20.926   1604
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.75 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 16.04 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -0.95 (0.22), residues: 1451
  helix:  0.15 (0.24), residues: 466
  sheet:  0.11 (0.34), residues: 242
  loop : -1.40 (0.23), residues: 743

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 497 
 TYR   0.030   0.002   TYR A 190 
 PHE   0.030   0.002   PHE C 308 
 TRP   0.022   0.002   TRP C  37 
 HIS   0.010   0.002   HIS A 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00571 (12120)
  covalent geometry    : angle       0.71384 (16387)
  hydrogen bonds       : bond        0.05279 (  443)
  hydrogen bonds       : angle       5.89313 ( 1269)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 111
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 ARG cc_start: 0.5926 (OUTLIER) cc_final: 0.5629 (ttp-110)
REVERT: A  334 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.6067 (t80)
REVERT: A  671 MET cc_start: 0.5677 (mtm) cc_final: 0.5325 (mtm)
REVERT: A  787 PHE cc_start: 0.6276 (m-80) cc_final: 0.6010 (m-80)
REVERT: B   29 PHE cc_start: 0.5230 (m-80) cc_final: 0.3489 (t80)
REVERT: B  212 TRP cc_start: 0.3498 (m100) cc_final: 0.3244 (m100)
  outliers start: 41
  outliers final: 28
  residues processed: 140
  average time/residue: 0.1063
  time to fit residues: 22.4034
Evaluate side-chains
  135 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 105
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  190 TYR
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  322 ASN
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  598 THR
Chi-restraints excluded: chain A residue  610 SER
Chi-restraints excluded: chain A residue  701 VAL
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue  330 THR
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 96 optimal weight:    8.9990
   chunk 77 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0570
   chunk 15 optimal weight:    1.9990
   chunk 98 optimal weight:   10.0000
   chunk 71 optimal weight:    9.9990
   chunk 136 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 123 optimal weight:   20.0000
   overall best weight:    1.1302

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

Flipped N/Q/H residues before XYZ refinement:
A 170 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5368 r_free = 0.5368 target = 0.291243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.5077 r_free = 0.5077 target = 0.248343 restraints weight = 12217.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.5096 rms_B_bonded: 3.50
r_work: 0.4594 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.4594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5656
moved from start:          0.3413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12120  Z= 0.146
  Angle     :  0.579  10.419  16387  Z= 0.297
  Chirality :  0.044   0.192   1817
  Planarity :  0.004   0.060   2085
  Dihedral  :  4.476  20.606   1604
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.03 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.39 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -0.68 (0.23), residues: 1451
  helix:  0.49 (0.24), residues: 469
  sheet:  0.09 (0.34), residues: 241
  loop : -1.25 (0.24), residues: 741

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 497 
 TYR   0.023   0.001   TYR A 190 
 PHE   0.030   0.001   PHE C 308 
 TRP   0.016   0.001   TRP C  37 
 HIS   0.006   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (12120)
  covalent geometry    : angle       0.57943 (16387)
  hydrogen bonds       : bond        0.03935 (  443)
  hydrogen bonds       : angle       5.40113 ( 1269)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 117
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 PHE cc_start: 0.6603 (OUTLIER) cc_final: 0.6002 (t80)
REVERT: A  497 ARG cc_start: 0.5228 (mmm160) cc_final: 0.3567 (ttt-90)
REVERT: A  787 PHE cc_start: 0.5777 (m-80) cc_final: 0.5499 (m-80)
REVERT: C   95 MET cc_start: 0.4049 (tpp) cc_final: 0.3835 (tpp)
REVERT: C  255 ARG cc_start: 0.5154 (ttp-170) cc_final: 0.4852 (ptm-80)
REVERT: C  425 PHE cc_start: 0.4356 (m-80) cc_final: 0.4086 (m-80)
REVERT: B   29 PHE cc_start: 0.5293 (m-80) cc_final: 0.3642 (t80)
REVERT: B  212 TRP cc_start: 0.3487 (m100) cc_final: 0.3202 (m100)
  outliers start: 31
  outliers final: 25
  residues processed: 137
  average time/residue: 0.1081
  time to fit residues: 22.2490
Evaluate side-chains
  139 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 113
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  322 ASN
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  515 THR
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  598 THR
Chi-restraints excluded: chain A residue  701 VAL
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 143 optimal weight:    4.9990
   chunk 133 optimal weight:    9.9990
   chunk 19 optimal weight:    0.8980
   chunk 75 optimal weight:    9.9990
   chunk 99 optimal weight:   20.0000
   chunk 107 optimal weight:    0.4980
   chunk 41 optimal weight:    0.9980
   chunk 120 optimal weight:    5.9990
   chunk 106 optimal weight:    6.9990
   chunk 110 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5380 r_free = 0.5380 target = 0.290559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 98)----------------|
| r_work = 0.4814 r_free = 0.4814 target = 0.217528 restraints weight = 12408.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.4757 rms_B_bonded: 2.56
r_work: 0.4549 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.4549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5650
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  12120  Z= 0.194
  Angle     :  0.654  12.127  16387  Z= 0.336
  Chirality :  0.045   0.204   1817
  Planarity :  0.005   0.062   2085
  Dihedral  :  4.717  20.846   1604
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 14.65
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.20 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.69 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -0.85 (0.22), residues: 1451
  helix:  0.26 (0.24), residues: 471
  sheet:  0.08 (0.35), residues: 223
  loop : -1.29 (0.23), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 497 
 TYR   0.028   0.002   TYR A 190 
 PHE   0.024   0.002   PHE C 308 
 TRP   0.020   0.002   TRP C  37 
 HIS   0.007   0.001   HIS A 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 (12120)
  covalent geometry    : angle       0.65392 (16387)
  hydrogen bonds       : bond        0.04580 (  443)
  hydrogen bonds       : angle       5.61399 ( 1269)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 113
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.6001 (t80)
REVERT: A  409 ASP cc_start: 0.6027 (OUTLIER) cc_final: 0.5707 (m-30)
REVERT: A  787 PHE cc_start: 0.6198 (m-80) cc_final: 0.5941 (m-80)
REVERT: C   95 MET cc_start: 0.4007 (tpp) cc_final: 0.3735 (tpp)
REVERT: B   23 MET cc_start: 0.3225 (ptm) cc_final: 0.2879 (ptm)
REVERT: B   29 PHE cc_start: 0.5078 (m-80) cc_final: 0.3721 (t80)
REVERT: B  212 TRP cc_start: 0.3270 (m100) cc_final: 0.2961 (m100)
  outliers start: 36
  outliers final: 29
  residues processed: 139
  average time/residue: 0.1075
  time to fit residues: 22.7517
Evaluate side-chains
  141 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 110
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  190 TYR
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  322 ASN
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  515 THR
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  598 THR
Chi-restraints excluded: chain A residue  701 VAL
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue  330 THR
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 104 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0170
   chunk 64 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 131 optimal weight:    0.0010
   chunk 26 optimal weight:    3.9990
   chunk 108 optimal weight:   20.0000
   chunk 76 optimal weight:    6.9990
   chunk 66 optimal weight:    0.8980
   chunk 100 optimal weight:    0.8980
   chunk 95 optimal weight:   30.0000
   overall best weight:    0.5624

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

Flipped N/Q/H residues before XYZ refinement:
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5420 r_free = 0.5420 target = 0.295961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.4895 r_free = 0.4895 target = 0.226074 restraints weight = 12276.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.4819 rms_B_bonded: 2.84
r_work: 0.4609 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.4609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5465
moved from start:          0.3689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12120  Z= 0.115
  Angle     :  0.556  11.138  16387  Z= 0.285
  Chirality :  0.043   0.205   1817
  Planarity :  0.004   0.061   2085
  Dihedral  :  4.265  18.812   1604
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.82 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 18.43 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -0.50 (0.23), residues: 1451
  helix:  0.62 (0.25), residues: 478
  sheet:  0.12 (0.34), residues: 241
  loop : -1.13 (0.24), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 497 
 TYR   0.019   0.001   TYR A 190 
 PHE   0.027   0.001   PHE C 308 
 TRP   0.015   0.001   TRP B 137 
 HIS   0.005   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (12120)
  covalent geometry    : angle       0.55601 (16387)
  hydrogen bonds       : bond        0.03443 (  443)
  hydrogen bonds       : angle       5.14445 ( 1269)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 123
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 PHE cc_start: 0.6591 (OUTLIER) cc_final: 0.5859 (t80)
REVERT: A  497 ARG cc_start: 0.5152 (mmm160) cc_final: 0.3674 (ttt-90)
REVERT: C   95 MET cc_start: 0.3898 (tpp) cc_final: 0.3636 (tpp)
REVERT: C  425 PHE cc_start: 0.4293 (m-80) cc_final: 0.4011 (m-80)
REVERT: B   23 MET cc_start: 0.3270 (ptm) cc_final: 0.2908 (ptm)
REVERT: B   29 PHE cc_start: 0.5081 (m-80) cc_final: 0.3651 (t80)
REVERT: B  195 PHE cc_start: 0.0896 (m-80) cc_final: 0.0667 (m-80)
  outliers start: 26
  outliers final: 23
  residues processed: 140
  average time/residue: 0.1044
  time to fit residues: 22.3866
Evaluate side-chains
  138 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  257 ASP
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  515 THR
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  598 THR
Chi-restraints excluded: chain A residue  701 VAL
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 142 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 115 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 120 optimal weight:    0.3980
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 199 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5407 r_free = 0.5407 target = 0.294186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4864 r_free = 0.4864 target = 0.221367 restraints weight = 12336.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.4798 rms_B_bonded: 2.52
r_work: 0.4621 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.4621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5543
moved from start:          0.3808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12120  Z= 0.145
  Angle     :  0.597  13.342  16387  Z= 0.306
  Chirality :  0.044   0.220   1817
  Planarity :  0.004   0.060   2085
  Dihedral  :  4.397  19.193   1604
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.79 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 18.36 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -0.53 (0.23), residues: 1451
  helix:  0.57 (0.24), residues: 477
  sheet:  0.03 (0.34), residues: 247
  loop : -1.11 (0.24), residues: 727

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 497 
 TYR   0.024   0.001   TYR A 190 
 PHE   0.026   0.001   PHE C 308 
 TRP   0.015   0.001   TRP C  37 
 HIS   0.013   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (12120)
  covalent geometry    : angle       0.59681 (16387)
  hydrogen bonds       : bond        0.03833 (  443)
  hydrogen bonds       : angle       5.23315 ( 1269)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6425 (mm-30)
REVERT: A  334 PHE cc_start: 0.6606 (OUTLIER) cc_final: 0.5937 (t80)
REVERT: A  497 ARG cc_start: 0.5138 (mmm160) cc_final: 0.3603 (ttt-90)
REVERT: C   95 MET cc_start: 0.4094 (tpp) cc_final: 0.3724 (tpp)
REVERT: C  425 PHE cc_start: 0.4103 (m-80) cc_final: 0.3792 (m-80)
REVERT: B   23 MET cc_start: 0.3345 (ptm) cc_final: 0.2988 (ptm)
REVERT: B   29 PHE cc_start: 0.5027 (m-80) cc_final: 0.3714 (t80)
  outliers start: 31
  outliers final: 26
  residues processed: 134
  average time/residue: 0.1051
  time to fit residues: 21.2469
Evaluate side-chains
  140 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 113
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  257 ASP
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  515 THR
Chi-restraints excluded: chain A residue  550 TYR
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  598 THR
Chi-restraints excluded: chain A residue  701 VAL
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  208 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 122 optimal weight:    0.9990
   chunk 139 optimal weight:    8.9990
   chunk 129 optimal weight:    3.9990
   chunk 95 optimal weight:   20.0000
   chunk 22 optimal weight:    0.9990
   chunk 114 optimal weight:    8.9990
   chunk 117 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 135 optimal weight:    0.9980
   chunk 136 optimal weight:    0.7980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5414 r_free = 0.5414 target = 0.295000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.4889 r_free = 0.4889 target = 0.226028 restraints weight = 12270.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.4836 rms_B_bonded: 2.69
r_work: 0.4612 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.4612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5481
moved from start:          0.3897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12120  Z= 0.135
  Angle     :  0.587  13.886  16387  Z= 0.298
  Chirality :  0.043   0.205   1817
  Planarity :  0.004   0.061   2085
  Dihedral  :  4.326  19.169   1604
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.58 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 18.58 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -0.48 (0.23), residues: 1451
  helix:  0.65 (0.24), residues: 475
  sheet:  0.09 (0.34), residues: 247
  loop : -1.10 (0.24), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 497 
 TYR   0.022   0.001   TYR A 190 
 PHE   0.028   0.001   PHE A 267 
 TRP   0.015   0.001   TRP C  37 
 HIS   0.003   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (12120)
  covalent geometry    : angle       0.58672 (16387)
  hydrogen bonds       : bond        0.03666 (  443)
  hydrogen bonds       : angle       5.17009 ( 1269)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4157.86 seconds
wall clock time: 71 minutes 57.84 seconds (4317.84 seconds total)