Starting phenix.real_space_refine
on Thu Sep 18 06:15:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g74_51109/09_2025/9g74_51109.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g74_51109/09_2025/9g74_51109.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9g74_51109/09_2025/9g74_51109.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g74_51109/09_2025/9g74_51109.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g74_51109/09_2025/9g74_51109.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g74_51109/09_2025/9g74_51109.cif"
  }
  resolution = 2.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.976
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     P      41      5.49       5
     S      77      5.16       5
     C    9200      2.51       5
     N    2584      2.21       5
     O    2780      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14683
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 7628
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 956, 7628
          Classifications: {'peptide': 956}
          Link IDs: {'PTRANS': 62, 'TRANS': 893}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 3127
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 393, 3127
          Classifications: {'peptide': 393}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 374}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 3119
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 392, 3119
          Classifications: {'peptide': 392}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 373}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "P"
      Number of atoms: 375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 375
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
    Chain: "T"
      Number of atoms: 405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 405
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 29
          Unusual residues: {' CA': 1, 'DCP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.13, per 1000 atoms: 0.21
  Number of scatterers: 14683
  At special positions: 0
  Unit cell: (108.9, 101.475, 147.675, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      1     19.99
     S      77     16.00
     P      41     15.00
     O    2780      8.00
     N    2584      7.00
     C    9200      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Conformation dependent library (CDL) restraints added in 494.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3248

  Finding SS restraints...
    Secondary structure from input PDB file:
      75 helices and 13 sheets defined
      49.5% alpha, 13.2% beta
      18 base pairs and 34 stacking pairs defined.
    Time for finding SS restraints: 1.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 71
      removed outlier: 3.617A  pdb=" N   GLN A  69 " --> pdb=" O   GLY A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 93
      removed outlier: 4.041A  pdb=" N   HIS A  93 " --> pdb=" O   HIS A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 130
    Processing helix  chain 'A' and resid 130 through 142
      removed outlier: 3.520A  pdb=" N   LEU A 134 " --> pdb=" O   SER A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 165
      No H-bonds generated for 'chain 'A' and resid 163 through 165'
    Processing helix  chain 'A' and resid 186 through 189
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 3.673A  pdb=" N   VAL A 212 " --> pdb=" O   SER A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 227
    Processing helix  chain 'A' and resid 253 through 259
    Processing helix  chain 'A' and resid 260 through 266
      removed outlier: 6.623A  pdb=" N   GLU A 263 " --> pdb=" O   HIS A 260 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   TYR A 265 " --> pdb=" O   ARG A 262 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU A 266 " --> pdb=" O   GLU A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 286
    Processing helix  chain 'A' and resid 288 through 299
    Processing helix  chain 'A' and resid 328 through 333
      removed outlier: 3.743A  pdb=" N   ILE A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 346
    Processing helix  chain 'A' and resid 363 through 370
    Processing helix  chain 'A' and resid 370 through 400
      Proline residue:  A 394  - end of helix
    Processing helix  chain 'A' and resid 402 through 413
      removed outlier: 4.101A  pdb=" N   LEU A 406 " --> pdb=" O   HIS A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 453
    Processing helix  chain 'A' and resid 454 through 464
      removed outlier: 3.778A  pdb=" N   SER A 457 " --> pdb=" O   GLN A 454 " (cutoff:3.500A)
      removed outlier: 5.111A  pdb=" N   GLY A 458 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ARG A 460 " --> pdb=" O   SER A 457 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   TYR A 461 " --> pdb=" O   GLY A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 533
      removed outlier: 3.669A  pdb=" N   LEU A 533 " --> pdb=" O   ARG A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 540
      removed outlier: 4.532A  pdb=" N   THR A 537 " --> pdb=" O   ARG A 534 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   ASP A 538 " --> pdb=" O   SER A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 557
      removed outlier: 3.535A  pdb=" N   LEU A 557 " --> pdb=" O   TRP A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 585
    Processing helix  chain 'A' and resid 629 through 645
    Processing helix  chain 'A' and resid 745 through 747
      No H-bonds generated for 'chain 'A' and resid 745 through 747'
    Processing helix  chain 'A' and resid 748 through 754
    Processing helix  chain 'A' and resid 764 through 788
      removed outlier: 5.085A  pdb=" N   PHE A 778 " --> pdb=" O   LYS A 774 " (cutoff:3.500A)
      removed outlier: 5.312A  pdb=" N   TRP A 779 " --> pdb=" O   MET A 775 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   LYS A 784 " --> pdb=" O   ARG A 780 " (cutoff:3.500A)
      removed outlier: 5.558A  pdb=" N   ARG A 785 " --> pdb=" O   ASN A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 806
    Processing helix  chain 'A' and resid 836 through 840
      removed outlier: 3.556A  pdb=" N   ALA A 840 " --> pdb=" O   TRP A 837 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 852 through 856
    Processing helix  chain 'A' and resid 871 through 886
      removed outlier: 3.556A  pdb=" N   ALA A 886 " --> pdb=" O   ASP A 882 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 892 through 900
    Processing helix  chain 'A' and resid 908 through 918
    Processing helix  chain 'A' and resid 920 through 934
      removed outlier: 3.839A  pdb=" N   ILE A 926 " --> pdb=" O   GLU A 922 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 936 through 948
    Processing helix  chain 'A' and resid 952 through 966
      removed outlier: 3.541A  pdb=" N   VAL A 966 " --> pdb=" O   GLN A 962 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1032 through 1045
    Processing helix  chain 'A' and resid 1058 through 1062
      removed outlier: 3.895A  pdb=" N   GLU A1062 " --> pdb=" O   ARG A1059 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1070 through 1102
      removed outlier: 4.102A  pdb=" N   VAL A1078 " --> pdb=" O   ARG A1074 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   VAL A1079 " --> pdb=" O   VAL A1075 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1123 through 1147
    Processing helix  chain 'A' and resid 1197 through 1206
    Processing helix  chain 'B' and resid 42 through 50
    Processing helix  chain 'B' and resid 56 through 60
      removed outlier: 3.504A  pdb=" N   LEU B  60 " --> pdb=" O   PRO B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 68
      removed outlier: 3.557A  pdb=" N   GLY B  68 " --> pdb=" O   ALA B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 94
    Processing helix  chain 'B' and resid 123 through 132
    Processing helix  chain 'B' and resid 137 through 151
    Processing helix  chain 'B' and resid 159 through 166
      removed outlier: 3.763A  pdb=" N   HIS B 166 " --> pdb=" O   GLY B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 174
    Processing helix  chain 'B' and resid 218 through 220
      No H-bonds generated for 'chain 'B' and resid 218 through 220'
    Processing helix  chain 'B' and resid 221 through 240
      removed outlier: 4.025A  pdb=" N   PHE B 240 " --> pdb=" O   TRP B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 245
      No H-bonds generated for 'chain 'B' and resid 243 through 245'
    Processing helix  chain 'B' and resid 282 through 289
    Processing helix  chain 'B' and resid 292 through 296
      removed outlier: 3.658A  pdb=" N   THR B 295 " --> pdb=" O   ASN B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 328
    Processing helix  chain 'B' and resid 365 through 383
      removed outlier: 3.571A  pdb=" N   ASN B 383 " --> pdb=" O   GLU B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 398 through 409
    Processing helix  chain 'B' and resid 418 through 424
      removed outlier: 4.003A  pdb=" N   LEU B 422 " --> pdb=" O   THR B 418 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLU B 423 " --> pdb=" O   GLU B 419 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 457
      removed outlier: 4.386A  pdb=" N   ARG B 446 " --> pdb=" O   ILE B 442 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   ASP B 447 " --> pdb=" O   SER B 443 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER B 457 " --> pdb=" O   LEU B 453 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 50
    Processing helix  chain 'C' and resid 61 through 68
      removed outlier: 3.643A  pdb=" N   GLY C  68 " --> pdb=" O   ALA C  64 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 93
    Processing helix  chain 'C' and resid 123 through 132
    Processing helix  chain 'C' and resid 137 through 151
    Processing helix  chain 'C' and resid 159 through 166
    Processing helix  chain 'C' and resid 166 through 174
    Processing helix  chain 'C' and resid 221 through 240
      removed outlier: 3.992A  pdb=" N   PHE C 240 " --> pdb=" O   TRP C 236 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 243 through 245
      No H-bonds generated for 'chain 'C' and resid 243 through 245'
    Processing helix  chain 'C' and resid 282 through 289
    Processing helix  chain 'C' and resid 315 through 327
    Processing helix  chain 'C' and resid 365 through 383
    Processing helix  chain 'C' and resid 391 through 393
      No H-bonds generated for 'chain 'C' and resid 391 through 393'
    Processing helix  chain 'C' and resid 398 through 409
    Processing helix  chain 'C' and resid 418 through 425
      removed outlier: 3.804A  pdb=" N   LEU C 422 " --> pdb=" O   THR C 418 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 444 through 458
    Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 170
      removed outlier: 3.757A  pdb=" N   TRP A 158 " --> pdb=" O   VAL A 170 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   TRP A 203 " --> pdb=" O   TYR A 161 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   LEU A 178 " --> pdb=" O   VAL A 250 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 417 through 420
    Processing sheet with id=AA3, first strand: chain 'A' and resid 587 through 588
    Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 596
      removed outlier: 4.350A  pdb=" N   PHE A 727 " --> pdb=" O   TYR A 717 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1107 through 1109
      removed outlier: 6.835A  pdb=" N   ARG A1116 " --> pdb=" O   CYS A1108 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 101
      removed outlier: 6.339A  pdb=" N   PHE B 100 " --> pdb=" O   ALA B 183 " (cutoff:3.500A)
      removed outlier: 8.593A  pdb=" N   ILE B 185 " --> pdb=" O   PHE B 100 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   ILE B 274 " --> pdb=" O   ASP B 315 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   TYR B 265 " --> pdb=" O   PRO B 273 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLU B 275 " --> pdb=" O   LEU B 263 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   LYS B 259 " --> pdb=" O   ASN B 279 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 108
    Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 122
      removed outlier: 3.834A  pdb=" N   GLY C 153 " --> pdb=" O   LEU C 121 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 300
    Processing sheet with id=AB1, first strand: chain 'B' and resid 387 through 389
      removed outlier: 6.859A  pdb=" N   VAL B 357 " --> pdb=" O   TRP B 388 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ALA B 358 " --> pdb=" O   VAL B 415 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 99 through 101
      removed outlier: 5.828A  pdb=" N   VAL C 309 " --> pdb=" O   LEU C 280 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   TYR C 265 " --> pdb=" O   PRO C 273 " (cutoff:3.500A)
      removed outlier: 5.135A  pdb=" N   LYS C 259 " --> pdb=" O   ASN C 279 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ALA C 250 " --> pdb=" O   LYS C 262 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 298 through 300
    Processing sheet with id=AB4, first strand: chain 'C' and resid 387 through 389
      removed outlier: 7.274A  pdb=" N   TRP C 388 " --> pdb=" O   ILE C 355 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   VAL C 357 " --> pdb=" O   TRP C 388 " (cutoff:3.500A)
      removed outlier: 6.019A  pdb=" N   LYS C 356 " --> pdb=" O   PHE C 413 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   VAL C 415 " --> pdb=" O   LYS C 356 " (cutoff:3.500A)
      removed outlier: 5.899A  pdb=" N   ALA C 358 " --> pdb=" O   VAL C 415 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   VAL C 417 " --> pdb=" O   ALA C 358 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ASP C 360 " --> pdb=" O   VAL C 417 " (cutoff:3.500A)

    688 hydrogen bonds defined for protein.
    1962 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      46 hydrogen bonds
      88 hydrogen bond angles
      0 basepair planarities
      18 basepair parallelities
      34 stacking parallelities
  Total time for adding SS restraints: 2.87

  Time building geometry restraints manager: 1.42 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 4232
        1.33 -     1.45: 2675
        1.45 -     1.57: 8016
        1.57 -     1.69: 79
        1.69 -     1.81: 120
  Bond restraints: 15122
  Sorted by residual:
  bond pdb=" C4  DCP A1301 "
       pdb=" C5  DCP A1301 "
    ideal  model  delta    sigma   weight residual
    1.426  1.384  0.042 1.20e-02 6.94e+03 1.20e+01
  bond pdb=" C6  DCP A1301 "
       pdb=" N1  DCP A1301 "
    ideal  model  delta    sigma   weight residual
    1.375  1.334  0.041 1.20e-02 6.94e+03 1.14e+01
  bond pdb=" CA  LEU B 377 "
       pdb=" C   LEU B 377 "
    ideal  model  delta    sigma   weight residual
    1.524  1.484  0.040 1.24e-02 6.50e+03 1.05e+01
  bond pdb=" O1B DCP A1301 "
       pdb=" PB  DCP A1301 "
    ideal  model  delta    sigma   weight residual
    1.477  1.508 -0.031 1.10e-02 8.26e+03 7.83e+00
  bond pdb=" O1A DCP A1301 "
       pdb=" PA  DCP A1301 "
    ideal  model  delta    sigma   weight residual
    1.477  1.503 -0.026 1.00e-02 1.00e+04 6.90e+00
  ... (remaining 15117 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.32: 20632
        3.32 -     6.64: 35
        6.64 -     9.95: 3
        9.95 -    13.27: 0
       13.27 -    16.59: 2
  Bond angle restraints: 20672
  Sorted by residual:
  angle pdb=" PB  DCP A1301 "
        pdb=" O3B DCP A1301 "
        pdb=" PG  DCP A1301 "
      ideal   model   delta    sigma   weight residual
     139.87  123.28   16.59 1.00e+00 1.00e+00 2.75e+02
  angle pdb=" PA  DCP A1301 "
        pdb=" O3A DCP A1301 "
        pdb=" PB  DCP A1301 "
      ideal   model   delta    sigma   weight residual
     136.83  122.11   14.72 1.00e+00 1.00e+00 2.17e+02
  angle pdb=" O1G DCP A1301 "
        pdb=" PG  DCP A1301 "
        pdb=" O3B DCP A1301 "
      ideal   model   delta    sigma   weight residual
     110.47  103.70    6.77 1.64e+00 3.70e-01 1.70e+01
  angle pdb=" C   THR A 836 "
        pdb=" CA  THR A 836 "
        pdb=" CB  THR A 836 "
      ideal   model   delta    sigma   weight residual
     110.37  103.74    6.63 1.64e+00 3.72e-01 1.64e+01
  angle pdb=" N   ASP A1162 "
        pdb=" CA  ASP A1162 "
        pdb=" C   ASP A1162 "
      ideal   model   delta    sigma   weight residual
     108.41  114.32   -5.91 1.61e+00 3.86e-01 1.35e+01
  ... (remaining 20667 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.53: 8186
       14.53 -    29.06: 510
       29.06 -    43.58: 137
       43.58 -    58.11: 93
       58.11 -    72.64: 6
  Dihedral angle restraints: 8932
    sinusoidal: 3908
      harmonic: 5024
  Sorted by residual:
  dihedral pdb=" CA  HIS B  51 "
           pdb=" C   HIS B  51 "
           pdb=" N   PHE B  52 "
           pdb=" CA  PHE B  52 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.62   18.38     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  ILE A1111 "
           pdb=" C   ILE A1111 "
           pdb=" N   HIS A1112 "
           pdb=" CA  HIS A1112 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.51   17.49     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" CA  TYR C 264 "
           pdb=" C   TYR C 264 "
           pdb=" N   TYR C 265 "
           pdb=" CA  TYR C 265 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.17   16.83     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 8929 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1625
       0.036 -    0.072: 453
       0.072 -    0.107: 123
       0.107 -    0.143: 39
       0.143 -    0.179: 4
  Chirality restraints: 2244
  Sorted by residual:
  chirality pdb=" CB  VAL A1115 "
            pdb=" CA  VAL A1115 "
            pdb=" CG1 VAL A1115 "
            pdb=" CG2 VAL A1115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.99e-01
  chirality pdb=" CB  ILE A1111 "
            pdb=" CA  ILE A1111 "
            pdb=" CG1 ILE A1111 "
            pdb=" CG2 ILE A1111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.33e-01
  chirality pdb=" CG  LEU B 377 "
            pdb=" CB  LEU B 377 "
            pdb=" CD1 LEU B 377 "
            pdb=" CD2 LEU B 377 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.62e-01
  ... (remaining 2241 not shown)

  Planarity restraints: 2526
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A  55 "    0.032 5.00e-02 4.00e+02   4.86e-02 3.78e+00
        pdb=" N   PRO A  56 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A  56 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A  56 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 766 "   -0.029 5.00e-02 4.00e+02   4.38e-02 3.06e+00
        pdb=" N   PRO A 767 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 767 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 767 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A1114 "    0.007 2.00e-02 2.50e+03   1.47e-02 2.17e+00
        pdb=" C   GLU A1114 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   GLU A1114 "    0.010 2.00e-02 2.50e+03
        pdb=" N   VAL A1115 "    0.009 2.00e-02 2.50e+03
  ... (remaining 2523 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.38: 42
        2.38 -     3.01: 7846
        3.01 -     3.64: 22461
        3.64 -     4.27: 34881
        4.27 -     4.90: 57724
  Nonbonded interactions: 122954
  Sorted by model distance:
  nonbonded pdb="CA    CA A1300 "
            pdb=" O1B DCP A1301 "
     model   vdw
     1.747 2.510
  nonbonded pdb="CA    CA A1300 "
            pdb=" O2G DCP A1301 "
     model   vdw
     2.036 2.510
  nonbonded pdb=" OD1 ASP A 868 "
            pdb="CA    CA A1300 "
     model   vdw
     2.200 2.510
  nonbonded pdb=" OG1 THR A 159 "
            pdb=" OG  SER A 205 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OD1 ASP A 810 "
            pdb=" OH  TYR A 815 "
     model   vdw
     2.229 3.040
  ... (remaining 122949 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
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 42 through 192 or resid 204 through 457))
  selection = (chain 'C' and resid 42 through 457)
}

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:             2.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     14.950
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.040
  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:6.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7116
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15122  Z= 0.185
  Angle     :  0.523  16.589  20672  Z= 0.322
  Chirality :  0.039   0.179   2244
  Planarity :  0.004   0.049   2526
  Dihedral  : 11.792  72.639   5684
  Min Nonbonded Distance : 1.747

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  3.51 %
    Favored  : 95.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  1.14 (0.21), residues: 1715
  helix:  1.57 (0.19), residues: 753
  sheet: -0.01 (0.33), residues: 237
  loop :  0.29 (0.24), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 780 
 TYR   0.012   0.001   TYR A 416 
 PHE   0.017   0.001   PHE C 228 
 TRP   0.010   0.001   TRP A 726 
 HIS   0.003   0.001   HIS A 783 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (15122)
  covalent geometry    : angle       0.52284 (20672)
  hydrogen bonds       : bond        0.17377 (  734)
  hydrogen bonds       : angle       6.62745 ( 2050)

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 330
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 MET cc_start: 0.7885 (mtm) cc_final: 0.7635 (mtm)
REVERT: A  357 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6236 (mt-10)
REVERT: A  441 MET cc_start: 0.7235 (tpt) cc_final: 0.6766 (tmm)
REVERT: A  451 ASP cc_start: 0.7178 (t0) cc_final: 0.6938 (t70)
REVERT: A  478 LYS cc_start: 0.5741 (mmtt) cc_final: 0.5279 (ptpt)
REVERT: A  515 SER cc_start: 0.7769 (t) cc_final: 0.7496 (t)
REVERT: A  531 GLN cc_start: 0.6430 (tp40) cc_final: 0.6219 (tp40)
REVERT: A  534 ARG cc_start: 0.7892 (ttt-90) cc_final: 0.7205 (ttm110)
REVERT: A 1197 ASP cc_start: 0.5774 (t0) cc_final: 0.5264 (p0)
REVERT: B  175 ASN cc_start: 0.7754 (m-40) cc_final: 0.7497 (m-40)
REVERT: B  299 ARG cc_start: 0.5919 (mtt180) cc_final: 0.5267 (mtt90)
REVERT: C  233 ARG cc_start: 0.6778 (mmm160) cc_final: 0.6475 (mmm160)
REVERT: C  256 LEU cc_start: 0.8076 (mp) cc_final: 0.7755 (tt)
REVERT: C  370 ARG cc_start: 0.7101 (ttm170) cc_final: 0.6280 (ttt-90)
REVERT: C  404 SER cc_start: 0.7222 (t) cc_final: 0.6922 (p)
REVERT: C  419 GLU cc_start: 0.6771 (mt-10) cc_final: 0.6082 (pm20)
  outliers start: 8
  outliers final: 5
  residues processed: 333
  average time/residue: 0.5901
  time to fit residues: 215.3070
Evaluate side-chains
  193 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 188
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain B residue  133 ASP
Chi-restraints excluded: chain C residue  205 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    4.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 221 GLN
A 431 GLN
** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1153 GLN
B  51 HIS
B 161 HIS
C  51 HIS
C 184 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.200050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.169360 restraints weight = 15807.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.4320 rms_B_bonded: 1.76
r_work: 0.4183 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.4082 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.4082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  15122  Z= 0.204
  Angle     :  0.621  10.704  20672  Z= 0.316
  Chirality :  0.044   0.277   2244
  Planarity :  0.005   0.048   2526
  Dihedral  : 13.203  68.795   2327
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 11.13 %
    Favored  : 85.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  1.11 (0.21), residues: 1715
  helix:  1.46 (0.19), residues: 764
  sheet:  0.20 (0.33), residues: 233
  loop :  0.28 (0.24), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 233 
 TYR   0.017   0.002   TYR A 416 
 PHE   0.023   0.002   PHE C 228 
 TRP   0.015   0.002   TRP A 896 
 HIS   0.006   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 (15122)
  covalent geometry    : angle       0.62123 (20672)
  hydrogen bonds       : bond        0.04650 (  734)
  hydrogen bonds       : angle       5.16119 ( 2050)

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 207
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 ILE cc_start: 0.6510 (mt) cc_final: 0.6151 (mt)
REVERT: A  172 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7567 (pt)
REVERT: A  280 MET cc_start: 0.8114 (mtm) cc_final: 0.7848 (mtm)
REVERT: A  380 ARG cc_start: 0.6884 (ttm170) cc_final: 0.6561 (mtm-85)
REVERT: A  478 LYS cc_start: 0.5822 (mmtt) cc_final: 0.5330 (pttt)
REVERT: A  515 SER cc_start: 0.7676 (t) cc_final: 0.7402 (t)
REVERT: A  534 ARG cc_start: 0.8013 (ttt-90) cc_final: 0.7121 (ttm110)
REVERT: A  888 MET cc_start: 0.7110 (ptt) cc_final: 0.6407 (tpp)
REVERT: A  938 SER cc_start: 0.8121 (p) cc_final: 0.7896 (m)
REVERT: A 1086 TYR cc_start: 0.6770 (t80) cc_final: 0.6400 (t80)
REVERT: A 1141 MET cc_start: 0.6851 (tpp) cc_final: 0.6631 (tpt)
REVERT: A 1170 GLU cc_start: 0.7470 (mt-10) cc_final: 0.6999 (mm-30)
REVERT: B  208 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7409 (mtmm)
REVERT: B  299 ARG cc_start: 0.5840 (mtt180) cc_final: 0.5143 (mtt90)
REVERT: B  393 GLU cc_start: 0.6873 (pt0) cc_final: 0.6378 (mt-10)
REVERT: C  107 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7347 (pp30)
REVERT: C  108 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7010 (mm-30)
REVERT: C  256 LEU cc_start: 0.7983 (mp) cc_final: 0.7530 (tt)
REVERT: C  404 SER cc_start: 0.7224 (t) cc_final: 0.6909 (p)
  outliers start: 51
  outliers final: 15
  residues processed: 236
  average time/residue: 0.5628
  time to fit residues: 146.7481
Evaluate side-chains
  192 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 173
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  822 VAL
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  892 THR
Chi-restraints excluded: chain A residue 1033 SER
Chi-restraints excluded: chain A residue 1109 ILE
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  208 LYS
Chi-restraints excluded: chain B residue  313 SER
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   56 THR
Chi-restraints excluded: chain C residue  107 GLN
Chi-restraints excluded: chain C residue  108 GLU
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  227 ASP
Chi-restraints excluded: chain C residue  293 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 140 optimal weight:    0.9990
   chunk 149 optimal weight:    3.9990
   chunk 133 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 60 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 101 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 527 HIS
A 546 HIS
** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 GLN
B 190 HIS
B 297 GLN
C  51 HIS
C 403 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.201711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.172211 restraints weight = 15973.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.4289 rms_B_bonded: 1.82
r_work: 0.4089 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3980 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.2241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15122  Z= 0.137
  Angle     :  0.546   9.628  20672  Z= 0.280
  Chirality :  0.041   0.224   2244
  Planarity :  0.004   0.044   2526
  Dihedral  : 13.110  68.632   2321
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 12.65 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  1.28 (0.21), residues: 1715
  helix:  1.64 (0.19), residues: 764
  sheet:  0.23 (0.34), residues: 230
  loop :  0.35 (0.24), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 638 
 TYR   0.034   0.002   TYR B 406 
 PHE   0.015   0.001   PHE C 228 
 TRP   0.017   0.001   TRP A 896 
 HIS   0.003   0.001   HIS A 783 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (15122)
  covalent geometry    : angle       0.54609 (20672)
  hydrogen bonds       : bond        0.03993 (  734)
  hydrogen bonds       : angle       4.94720 ( 2050)

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 188
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 ILE cc_start: 0.6571 (mt) cc_final: 0.6224 (mt)
REVERT: A  280 MET cc_start: 0.8048 (mtm) cc_final: 0.7824 (mtm)
REVERT: A  380 ARG cc_start: 0.6952 (ttm170) cc_final: 0.6511 (mtm-85)
REVERT: A  478 LYS cc_start: 0.5819 (mmtt) cc_final: 0.5301 (pttt)
REVERT: A  515 SER cc_start: 0.7460 (t) cc_final: 0.7183 (t)
REVERT: A  888 MET cc_start: 0.7105 (ptt) cc_final: 0.6265 (tpp)
REVERT: A  938 SER cc_start: 0.8051 (p) cc_final: 0.7845 (m)
REVERT: A 1086 TYR cc_start: 0.6692 (t80) cc_final: 0.6347 (t80)
REVERT: A 1141 MET cc_start: 0.6807 (tpp) cc_final: 0.6559 (tpt)
REVERT: B  208 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7336 (mtmm)
REVERT: B  242 MET cc_start: 0.7361 (mmm) cc_final: 0.7147 (mmp)
REVERT: B  299 ARG cc_start: 0.5754 (mtt180) cc_final: 0.4879 (mtt90)
REVERT: C  107 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7325 (pp30)
REVERT: C  108 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.6920 (mm-30)
REVERT: C  256 LEU cc_start: 0.7933 (mp) cc_final: 0.7476 (tt)
REVERT: C  404 SER cc_start: 0.7226 (t) cc_final: 0.6908 (p)
  outliers start: 45
  outliers final: 21
  residues processed: 216
  average time/residue: 0.5682
  time to fit residues: 135.7660
Evaluate side-chains
  195 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 171
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  754 ASP
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  836 THR
Chi-restraints excluded: chain A residue  892 THR
Chi-restraints excluded: chain A residue 1033 SER
Chi-restraints excluded: chain A residue 1081 SER
Chi-restraints excluded: chain B residue  208 LYS
Chi-restraints excluded: chain B residue  313 SER
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  107 GLN
Chi-restraints excluded: chain C residue  108 GLU
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  227 ASP
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  313 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 154 optimal weight:    0.0670
   chunk 147 optimal weight:    4.9990
   chunk 160 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 172 optimal weight:    0.6980
   chunk 166 optimal weight:    1.9990
   chunk 124 optimal weight:    0.5980
   chunk 116 optimal weight:    0.6980
   chunk 171 optimal weight:    3.9990
   chunk 167 optimal weight:    4.9990
   overall best weight:    0.8120

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

Flipped N/Q/H residues before XYZ refinement:
** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 297 GLN
C  51 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4607 r_free = 0.4607 target = 0.201709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.171372 restraints weight = 15924.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.4346 rms_B_bonded: 1.75
r_work: 0.4208 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.4105 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.4105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  15122  Z= 0.132
  Angle     :  0.541   9.343  20672  Z= 0.275
  Chirality :  0.041   0.320   2244
  Planarity :  0.004   0.045   2526
  Dihedral  : 13.088  68.735   2321
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 13.91 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  1.34 (0.21), residues: 1715
  helix:  1.64 (0.19), residues: 771
  sheet:  0.38 (0.34), residues: 232
  loop :  0.37 (0.25), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 902 
 TYR   0.023   0.002   TYR B 406 
 PHE   0.014   0.001   PHE C 228 
 TRP   0.017   0.001   TRP A 896 
 HIS   0.003   0.001   HIS A 783 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (15122)
  covalent geometry    : angle       0.54091 (20672)
  hydrogen bonds       : bond        0.03783 (  734)
  hydrogen bonds       : angle       4.81279 ( 2050)

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 179
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 ILE cc_start: 0.6495 (mt) cc_final: 0.6156 (mt)
REVERT: A  280 MET cc_start: 0.8004 (mtm) cc_final: 0.7780 (mtm)
REVERT: A  380 ARG cc_start: 0.6793 (ttm170) cc_final: 0.6494 (mtm-85)
REVERT: A  478 LYS cc_start: 0.5768 (mmtt) cc_final: 0.5359 (pttt)
REVERT: A  515 SER cc_start: 0.7558 (t) cc_final: 0.7273 (t)
REVERT: A  542 LYS cc_start: 0.6071 (tttm) cc_final: 0.5730 (tttm)
REVERT: A  888 MET cc_start: 0.7067 (ptt) cc_final: 0.6343 (tpp)
REVERT: A  919 ILE cc_start: 0.7373 (pt) cc_final: 0.7021 (pp)
REVERT: A  938 SER cc_start: 0.8023 (p) cc_final: 0.7815 (m)
REVERT: A 1086 TYR cc_start: 0.6704 (t80) cc_final: 0.6425 (t80)
REVERT: A 1141 MET cc_start: 0.6686 (tpp) cc_final: 0.6444 (tpt)
REVERT: B  299 ARG cc_start: 0.5854 (mtt180) cc_final: 0.5052 (mtt90)
REVERT: B  393 GLU cc_start: 0.6845 (pt0) cc_final: 0.6173 (mt-10)
REVERT: C  107 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7294 (pp30)
REVERT: C  108 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.6865 (mm-30)
REVERT: C  256 LEU cc_start: 0.7942 (mp) cc_final: 0.7590 (tt)
REVERT: C  370 ARG cc_start: 0.7675 (ttm170) cc_final: 0.6731 (ttt-90)
REVERT: C  404 SER cc_start: 0.7249 (t) cc_final: 0.6964 (p)
  outliers start: 41
  outliers final: 27
  residues processed: 203
  average time/residue: 0.5792
  time to fit residues: 129.9837
Evaluate side-chains
  195 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 166
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  822 VAL
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  892 THR
Chi-restraints excluded: chain A residue 1081 SER
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  313 SER
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  360 ASP
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   56 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  107 GLN
Chi-restraints excluded: chain C residue  108 GLU
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  217 THR
Chi-restraints excluded: chain C residue  227 ASP
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  305 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 159 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9990
   chunk 118 optimal weight:    7.9990
   chunk 131 optimal weight:    5.9990
   chunk 137 optimal weight:    4.9990
   chunk 107 optimal weight:    3.9990
   chunk 93 optimal weight:    5.9990
   chunk 146 optimal weight:    4.9990
   chunk 144 optimal weight:   10.0000
   chunk 100 optimal weight:    1.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1080 GLN
B 113 GLN
B 297 GLN
C  51 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.194772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.163375 restraints weight = 15992.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.4260 rms_B_bonded: 1.76
r_work: 0.4126 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.4029 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.2876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.063  15122  Z= 0.325
  Angle     :  0.734   8.971  20672  Z= 0.371
  Chirality :  0.049   0.263   2244
  Planarity :  0.006   0.056   2526
  Dihedral  : 13.622  72.144   2321
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 13.58 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.61 (0.20), residues: 1715
  helix:  1.08 (0.19), residues: 763
  sheet: -0.06 (0.33), residues: 232
  loop : -0.02 (0.24), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 780 
 TYR   0.024   0.003   TYR A 133 
 PHE   0.020   0.003   PHE C 228 
 TRP   0.031   0.002   TRP A 468 
 HIS   0.006   0.001   HIS A 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00762 (15122)
  covalent geometry    : angle       0.73362 (20672)
  hydrogen bonds       : bond        0.05207 (  734)
  hydrogen bonds       : angle       5.34763 ( 2050)

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 181
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 ARG cc_start: 0.6860 (ttm170) cc_final: 0.6349 (mtm-85)
REVERT: A  461 TYR cc_start: 0.5449 (p90) cc_final: 0.5032 (p90)
REVERT: A  478 LYS cc_start: 0.5705 (mmtt) cc_final: 0.5389 (pttt)
REVERT: A  515 SER cc_start: 0.7804 (t) cc_final: 0.7551 (t)
REVERT: A  532 GLN cc_start: 0.7832 (tm130) cc_final: 0.7455 (tm-30)
REVERT: A  534 ARG cc_start: 0.8032 (ttt180) cc_final: 0.7080 (ttm110)
REVERT: A  542 LYS cc_start: 0.6119 (tttm) cc_final: 0.5758 (tttt)
REVERT: A  888 MET cc_start: 0.7117 (ptt) cc_final: 0.6251 (tpp)
REVERT: A  919 ILE cc_start: 0.7524 (pt) cc_final: 0.7230 (pp)
REVERT: A  938 SER cc_start: 0.8114 (p) cc_final: 0.7898 (m)
REVERT: A 1170 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6839 (mm-30)
REVERT: B  208 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7521 (mtmm)
REVERT: B  223 SER cc_start: 0.7682 (t) cc_final: 0.7346 (m)
REVERT: B  299 ARG cc_start: 0.5934 (mtt180) cc_final: 0.5201 (mtt90)
REVERT: C  107 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7306 (pp30)
REVERT: C  108 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.6855 (mm-30)
REVERT: C  256 LEU cc_start: 0.7989 (mp) cc_final: 0.7674 (tt)
REVERT: C  360 ASP cc_start: 0.7674 (m-30) cc_final: 0.7072 (m-30)
REVERT: C  370 ARG cc_start: 0.7830 (ttm170) cc_final: 0.6786 (ttt-90)
REVERT: C  382 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6826 (mm-30)
REVERT: C  404 SER cc_start: 0.7279 (t) cc_final: 0.7003 (p)
REVERT: C  423 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6327 (mt-10)
  outliers start: 71
  outliers final: 33
  residues processed: 233
  average time/residue: 0.5690
  time to fit residues: 146.6136
Evaluate side-chains
  205 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 167
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  221 GLN
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  822 VAL
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  836 THR
Chi-restraints excluded: chain A residue 1076 ASN
Chi-restraints excluded: chain A residue 1119 VAL
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  208 LYS
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain B residue  313 SER
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   56 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  107 GLN
Chi-restraints excluded: chain C residue  108 GLU
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  227 ASP
Chi-restraints excluded: chain C residue  248 SER
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  305 VAL
Chi-restraints excluded: chain C residue  382 GLU
Chi-restraints excluded: chain C residue  423 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 116 optimal weight:    0.8980
   chunk 155 optimal weight:    0.8980
   chunk 131 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 119 optimal weight:    0.0020
   chunk 108 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 104 optimal weight:    0.0270
   overall best weight:    0.5046

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

Flipped N/Q/H residues before XYZ refinement:
** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 253 GLN
C  51 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4602 r_free = 0.4602 target = 0.201165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.171157 restraints weight = 15906.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.4281 rms_B_bonded: 1.67
r_work: 0.4106 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3999 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15122  Z= 0.120
  Angle     :  0.559  12.879  20672  Z= 0.282
  Chirality :  0.041   0.346   2244
  Planarity :  0.005   0.048   2526
  Dihedral  : 13.360  71.026   2321
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 16.56 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  1.09 (0.21), residues: 1715
  helix:  1.51 (0.19), residues: 764
  sheet:  0.10 (0.35), residues: 228
  loop :  0.22 (0.24), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 638 
 TYR   0.042   0.002   TYR B 406 
 PHE   0.014   0.001   PHE C 228 
 TRP   0.022   0.001   TRP A 468 
 HIS   0.004   0.001   HIS A 783 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (15122)
  covalent geometry    : angle       0.55889 (20672)
  hydrogen bonds       : bond        0.03679 (  734)
  hydrogen bonds       : angle       4.89569 ( 2050)

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 188
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
REVERT: A  380 ARG cc_start: 0.6864 (ttm170) cc_final: 0.6503 (mtm-85)
REVERT: A  461 TYR cc_start: 0.5183 (p90) cc_final: 0.4871 (p90)
REVERT: A  478 LYS cc_start: 0.5638 (mmtt) cc_final: 0.5316 (pttt)
REVERT: A  515 SER cc_start: 0.7685 (t) cc_final: 0.7415 (t)
REVERT: A  532 GLN cc_start: 0.7835 (tm130) cc_final: 0.7395 (tm-30)
REVERT: A  542 LYS cc_start: 0.6072 (tttm) cc_final: 0.5724 (tttt)
REVERT: A  752 MET cc_start: 0.7494 (tpt) cc_final: 0.7242 (mmt)
REVERT: A  888 MET cc_start: 0.7074 (ptt) cc_final: 0.6247 (tpp)
REVERT: A 1086 TYR cc_start: 0.6721 (t80) cc_final: 0.6439 (t80)
REVERT: A 1170 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6800 (mm-30)
REVERT: B  223 SER cc_start: 0.7590 (t) cc_final: 0.7307 (m)
REVERT: B  297 GLN cc_start: 0.7351 (mt0) cc_final: 0.7096 (mt0)
REVERT: B  299 ARG cc_start: 0.5869 (mtt180) cc_final: 0.5036 (mtt90)
REVERT: B  393 GLU cc_start: 0.6922 (pt0) cc_final: 0.6297 (mt-10)
REVERT: B  401 GLN cc_start: 0.6798 (mt0) cc_final: 0.6468 (tm-30)
REVERT: C  108 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.6837 (mm-30)
REVERT: C  256 LEU cc_start: 0.8003 (mp) cc_final: 0.7636 (tt)
REVERT: C  370 ARG cc_start: 0.7781 (ttm170) cc_final: 0.6827 (ttt-90)
REVERT: C  382 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6732 (mm-30)
REVERT: C  404 SER cc_start: 0.7253 (t) cc_final: 0.6969 (p)
  outliers start: 42
  outliers final: 19
  residues processed: 218
  average time/residue: 0.5529
  time to fit residues: 133.4443
Evaluate side-chains
  196 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 175
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  822 VAL
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue 1033 SER
Chi-restraints excluded: chain A residue 1204 LEU
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  313 SER
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   56 THR
Chi-restraints excluded: chain C residue  108 GLU
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  217 THR
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  305 VAL
Chi-restraints excluded: chain C residue  382 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0270
   chunk 51 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 77 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 113 optimal weight:    2.9990
   chunk 103 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   overall best weight:    1.4046

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

Flipped N/Q/H residues before XYZ refinement:
** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 175 ASN
B 253 GLN
B 297 GLN
C  51 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.198618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.167888 restraints weight = 15701.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.4311 rms_B_bonded: 1.73
r_work: 0.4173 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.4072 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15122  Z= 0.175
  Angle     :  0.597  10.269  20672  Z= 0.301
  Chirality :  0.042   0.203   2244
  Planarity :  0.005   0.047   2526
  Dihedral  : 13.417  71.460   2321
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 16.62 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  1.07 (0.21), residues: 1715
  helix:  1.52 (0.19), residues: 764
  sheet:  0.02 (0.35), residues: 228
  loop :  0.20 (0.24), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 220 
 TYR   0.041   0.002   TYR B 406 
 PHE   0.016   0.002   PHE C 228 
 TRP   0.032   0.001   TRP A 468 
 HIS   0.004   0.001   HIS A 783 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 (15122)
  covalent geometry    : angle       0.59727 (20672)
  hydrogen bonds       : bond        0.04046 (  734)
  hydrogen bonds       : angle       4.95573 ( 2050)

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 177
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 LYS cc_start: 0.8085 (tmtt) cc_final: 0.7867 (tptp)
REVERT: A  380 ARG cc_start: 0.6766 (ttm170) cc_final: 0.6391 (mtm-85)
REVERT: A  461 TYR cc_start: 0.5321 (p90) cc_final: 0.4926 (p90)
REVERT: A  478 LYS cc_start: 0.5640 (mmtt) cc_final: 0.5293 (pttt)
REVERT: A  515 SER cc_start: 0.7767 (t) cc_final: 0.7498 (t)
REVERT: A  532 GLN cc_start: 0.7833 (tm130) cc_final: 0.7390 (tm-30)
REVERT: A  542 LYS cc_start: 0.6168 (tttm) cc_final: 0.5756 (tttt)
REVERT: A  888 MET cc_start: 0.6997 (ptt) cc_final: 0.6180 (tpp)
REVERT: A  919 ILE cc_start: 0.7381 (pt) cc_final: 0.6973 (pp)
REVERT: A 1086 TYR cc_start: 0.6875 (t80) cc_final: 0.6571 (t80)
REVERT: A 1170 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6805 (mm-30)
REVERT: B  223 SER cc_start: 0.7611 (t) cc_final: 0.7315 (m)
REVERT: B  299 ARG cc_start: 0.5916 (mtt180) cc_final: 0.5181 (mtt90)
REVERT: B  401 GLN cc_start: 0.6695 (mt0) cc_final: 0.6442 (tm-30)
REVERT: C  107 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7244 (pp30)
REVERT: C  108 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.6781 (mm-30)
REVERT: C  256 LEU cc_start: 0.8047 (mp) cc_final: 0.7686 (tt)
REVERT: C  360 ASP cc_start: 0.7751 (m-30) cc_final: 0.7067 (m-30)
REVERT: C  370 ARG cc_start: 0.7781 (ttm170) cc_final: 0.6805 (ttt-90)
REVERT: C  382 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6732 (mm-30)
REVERT: C  404 SER cc_start: 0.7208 (t) cc_final: 0.6909 (p)
REVERT: C  423 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6154 (mt-10)
  outliers start: 48
  outliers final: 27
  residues processed: 213
  average time/residue: 0.5670
  time to fit residues: 133.7001
Evaluate side-chains
  202 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 171
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  221 GLN
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue 1126 ARG
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  313 SER
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  386 SER
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   56 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  107 GLN
Chi-restraints excluded: chain C residue  108 GLU
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  227 ASP
Chi-restraints excluded: chain C residue  248 SER
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  305 VAL
Chi-restraints excluded: chain C residue  382 GLU
Chi-restraints excluded: chain C residue  423 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 123 optimal weight:    0.4980
   chunk 102 optimal weight:    3.9990
   chunk 142 optimal weight:    4.9990
   chunk 98 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 159 optimal weight:    5.9990
   chunk 132 optimal weight:    7.9990
   chunk 120 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 175 ASN
B 253 GLN
B 297 GLN
C  51 HIS
C 283 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.200671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.170738 restraints weight = 15903.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.4342 rms_B_bonded: 1.73
r_work: 0.4200 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.4095 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.4095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15122  Z= 0.133
  Angle     :  0.562  11.134  20672  Z= 0.284
  Chirality :  0.041   0.154   2244
  Planarity :  0.005   0.047   2526
  Dihedral  : 13.342  71.401   2321
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 17.28 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  1.20 (0.21), residues: 1715
  helix:  1.63 (0.19), residues: 765
  sheet: -0.01 (0.35), residues: 231
  loop :  0.31 (0.24), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 638 
 TYR   0.036   0.002   TYR B 406 
 PHE   0.015   0.001   PHE C 228 
 TRP   0.037   0.001   TRP A 468 
 HIS   0.004   0.001   HIS A 783 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (15122)
  covalent geometry    : angle       0.56161 (20672)
  hydrogen bonds       : bond        0.03693 (  734)
  hydrogen bonds       : angle       4.83455 ( 2050)

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 180
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LYS cc_start: 0.8111 (tmtt) cc_final: 0.7911 (tptp)
REVERT: A  380 ARG cc_start: 0.6820 (ttm170) cc_final: 0.6475 (mtm-85)
REVERT: A  461 TYR cc_start: 0.5285 (p90) cc_final: 0.4892 (p90)
REVERT: A  478 LYS cc_start: 0.5631 (mmtt) cc_final: 0.5294 (pttt)
REVERT: A  515 SER cc_start: 0.7777 (t) cc_final: 0.7522 (t)
REVERT: A  532 GLN cc_start: 0.7816 (tm130) cc_final: 0.7411 (tm-30)
REVERT: A  542 LYS cc_start: 0.6158 (tttm) cc_final: 0.5752 (tttt)
REVERT: A  604 LEU cc_start: 0.8030 (mt) cc_final: 0.7821 (tp)
REVERT: A  855 MET cc_start: 0.8030 (mmm) cc_final: 0.7612 (mmm)
REVERT: A  888 MET cc_start: 0.6966 (ptt) cc_final: 0.6174 (tpp)
REVERT: A  919 ILE cc_start: 0.7374 (pt) cc_final: 0.6987 (pp)
REVERT: A 1086 TYR cc_start: 0.6867 (t80) cc_final: 0.6559 (t80)
REVERT: A 1170 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6856 (mm-30)
REVERT: A 1196 LEU cc_start: 0.7500 (mp) cc_final: 0.7214 (mt)
REVERT: B  223 SER cc_start: 0.7570 (t) cc_final: 0.7291 (m)
REVERT: B  299 ARG cc_start: 0.5934 (mtt180) cc_final: 0.5167 (mtt90)
REVERT: B  393 GLU cc_start: 0.6974 (pt0) cc_final: 0.6287 (mt-10)
REVERT: C  107 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7197 (pp30)
REVERT: C  108 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.6755 (mm-30)
REVERT: C  256 LEU cc_start: 0.8084 (mp) cc_final: 0.7716 (tt)
REVERT: C  360 ASP cc_start: 0.7779 (m-30) cc_final: 0.7245 (m-30)
REVERT: C  382 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6714 (mm-30)
REVERT: C  404 SER cc_start: 0.7228 (t) cc_final: 0.6938 (p)
REVERT: C  423 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6154 (mt-10)
  outliers start: 41
  outliers final: 25
  residues processed: 209
  average time/residue: 0.5243
  time to fit residues: 121.7423
Evaluate side-chains
  204 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 175
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  221 GLN
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  822 VAL
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue 1126 ARG
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  313 SER
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  386 SER
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   56 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  107 GLN
Chi-restraints excluded: chain C residue  108 GLU
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  217 THR
Chi-restraints excluded: chain C residue  248 SER
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  305 VAL
Chi-restraints excluded: chain C residue  382 GLU
Chi-restraints excluded: chain C residue  423 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 144 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 125 optimal weight:    1.9990
   chunk 137 optimal weight:    4.9990
   chunk 21 optimal weight:    0.5980
   chunk 148 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 124 optimal weight:    0.8980
   chunk 69 optimal weight:    6.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  51 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4599 r_free = 0.4599 target = 0.200835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.170845 restraints weight = 15847.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.4282 rms_B_bonded: 1.72
r_work: 0.4097 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3985 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.3037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15122  Z= 0.135
  Angle     :  0.561  10.085  20672  Z= 0.284
  Chirality :  0.041   0.156   2244
  Planarity :  0.005   0.047   2526
  Dihedral  : 13.317  71.164   2321
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 17.68 %
    Favored  : 79.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  1.23 (0.21), residues: 1715
  helix:  1.64 (0.19), residues: 769
  sheet:  0.01 (0.35), residues: 231
  loop :  0.33 (0.24), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 638 
 TYR   0.034   0.002   TYR B 406 
 PHE   0.030   0.001   PHE B 228 
 TRP   0.040   0.001   TRP A 468 
 HIS   0.004   0.001   HIS A 783 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (15122)
  covalent geometry    : angle       0.56144 (20672)
  hydrogen bonds       : bond        0.03712 (  734)
  hydrogen bonds       : angle       4.80083 ( 2050)

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 180
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6765 (tm-30)
REVERT: A   92 LYS cc_start: 0.8167 (tmtt) cc_final: 0.7921 (tptp)
REVERT: A  353 LYS cc_start: 0.8171 (ptmt) cc_final: 0.7964 (ptmt)
REVERT: A  478 LYS cc_start: 0.5649 (mmtt) cc_final: 0.5287 (pttt)
REVERT: A  515 SER cc_start: 0.7722 (t) cc_final: 0.7454 (t)
REVERT: A  532 GLN cc_start: 0.7806 (tm130) cc_final: 0.7368 (tm-30)
REVERT: A  542 LYS cc_start: 0.6124 (tttm) cc_final: 0.5716 (tttt)
REVERT: A  604 LEU cc_start: 0.8049 (mt) cc_final: 0.7836 (tp)
REVERT: A  855 MET cc_start: 0.8042 (mmm) cc_final: 0.7612 (mmm)
REVERT: A  888 MET cc_start: 0.7031 (ptt) cc_final: 0.6192 (tpp)
REVERT: A 1170 GLU cc_start: 0.7484 (mt-10) cc_final: 0.6852 (mm-30)
REVERT: A 1196 LEU cc_start: 0.7506 (mp) cc_final: 0.7238 (mt)
REVERT: B   96 ARG cc_start: 0.8150 (mmp80) cc_final: 0.7823 (mmp-170)
REVERT: B  223 SER cc_start: 0.7606 (t) cc_final: 0.7324 (m)
REVERT: B  299 ARG cc_start: 0.5912 (mtt180) cc_final: 0.5058 (mtt90)
REVERT: C  107 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7220 (pp30)
REVERT: C  108 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.6806 (mm-30)
REVERT: C  256 LEU cc_start: 0.7975 (mp) cc_final: 0.7673 (tt)
REVERT: C  315 ASP cc_start: 0.7493 (t70) cc_final: 0.6944 (t0)
REVERT: C  382 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6595 (mm-30)
REVERT: C  404 SER cc_start: 0.7243 (t) cc_final: 0.6950 (p)
  outliers start: 41
  outliers final: 26
  residues processed: 208
  average time/residue: 0.5541
  time to fit residues: 127.5240
Evaluate side-chains
  205 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 176
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  221 GLN
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  822 VAL
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue 1126 ARG
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  313 SER
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  386 SER
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   56 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  107 GLN
Chi-restraints excluded: chain C residue  108 GLU
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  217 THR
Chi-restraints excluded: chain C residue  248 SER
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  305 VAL
Chi-restraints excluded: chain C residue  382 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 62 optimal weight:    0.3980
   chunk 131 optimal weight:    4.9990
   chunk 170 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9990
   chunk 117 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 127 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 401 GLN
C  51 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.201358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.171475 restraints weight = 15817.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.4351 rms_B_bonded: 1.71
r_work: 0.4210 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.4108 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.4108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.3100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15122  Z= 0.131
  Angle     :  0.573  12.741  20672  Z= 0.288
  Chirality :  0.041   0.165   2244
  Planarity :  0.004   0.047   2526
  Dihedral  : 13.293  71.070   2321
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.54 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  1.22 (0.21), residues: 1715
  helix:  1.60 (0.19), residues: 776
  sheet:  0.03 (0.34), residues: 231
  loop :  0.34 (0.24), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 638 
 TYR   0.032   0.002   TYR B 406 
 PHE   0.028   0.001   PHE B 228 
 TRP   0.033   0.001   TRP A 468 
 HIS   0.004   0.001   HIS A 783 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (15122)
  covalent geometry    : angle       0.57282 (20672)
  hydrogen bonds       : bond        0.03666 (  734)
  hydrogen bonds       : angle       4.78334 ( 2050)

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 180
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6813 (tm-30)
REVERT: A   92 LYS cc_start: 0.8131 (tmtt) cc_final: 0.7905 (tptp)
REVERT: A  353 LYS cc_start: 0.8212 (ptmt) cc_final: 0.8011 (ptmt)
REVERT: A  468 TRP cc_start: 0.7271 (p-90) cc_final: 0.6761 (p-90)
REVERT: A  478 LYS cc_start: 0.5687 (mmtt) cc_final: 0.5321 (pttt)
REVERT: A  515 SER cc_start: 0.7766 (t) cc_final: 0.7518 (t)
REVERT: A  532 GLN cc_start: 0.7780 (tm130) cc_final: 0.7352 (tm-30)
REVERT: A  542 LYS cc_start: 0.6218 (tttm) cc_final: 0.5834 (tttt)
REVERT: A  855 MET cc_start: 0.8023 (mmm) cc_final: 0.7585 (mmm)
REVERT: A  888 MET cc_start: 0.6945 (ptt) cc_final: 0.6157 (tpp)
REVERT: A 1196 LEU cc_start: 0.7521 (mp) cc_final: 0.7222 (mt)
REVERT: B   96 ARG cc_start: 0.8124 (mmp80) cc_final: 0.7800 (mmp-170)
REVERT: B  223 SER cc_start: 0.7509 (t) cc_final: 0.7232 (m)
REVERT: B  299 ARG cc_start: 0.5908 (mtt180) cc_final: 0.5136 (mtt90)
REVERT: C  107 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7191 (pp30)
REVERT: C  108 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.6672 (mm-30)
REVERT: C  256 LEU cc_start: 0.8006 (mp) cc_final: 0.7716 (tt)
REVERT: C  315 ASP cc_start: 0.7449 (t70) cc_final: 0.6929 (t0)
REVERT: C  404 SER cc_start: 0.7214 (t) cc_final: 0.6938 (p)
  outliers start: 36
  outliers final: 27
  residues processed: 207
  average time/residue: 0.5728
  time to fit residues: 131.2104
Evaluate side-chains
  205 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 176
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  221 GLN
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  822 VAL
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  313 SER
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  386 SER
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   56 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  107 GLN
Chi-restraints excluded: chain C residue  108 GLU
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  217 THR
Chi-restraints excluded: chain C residue  248 SER
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  305 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 165 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 148 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0870
   chunk 92 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 150 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0270
   overall best weight:    0.5820

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 175 ASN
B 401 GLN
C  51 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.202696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.172714 restraints weight = 15733.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.4303 rms_B_bonded: 1.79
r_work: 0.4122 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.4016 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.4016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.3152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15122  Z= 0.118
  Angle     :  0.564  12.487  20672  Z= 0.282
  Chirality :  0.040   0.158   2244
  Planarity :  0.004   0.046   2526
  Dihedral  : 13.235  70.668   2321
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 18.48 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  1.30 (0.21), residues: 1715
  helix:  1.66 (0.19), residues: 776
  sheet:  0.07 (0.34), residues: 231
  loop :  0.38 (0.24), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 638 
 TYR   0.029   0.002   TYR B 406 
 PHE   0.026   0.001   PHE B 228 
 TRP   0.029   0.001   TRP A 468 
 HIS   0.003   0.001   HIS A 783 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (15122)
  covalent geometry    : angle       0.56365 (20672)
  hydrogen bonds       : bond        0.03537 (  734)
  hydrogen bonds       : angle       4.71908 ( 2050)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5595.20 seconds
wall clock time: 96 minutes 1.46 seconds (5761.46 seconds total)