Starting phenix.real_space_refine
on Sat Aug 23 07:46:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6m5v_30094/08_2025/6m5v_30094.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6m5v_30094/08_2025/6m5v_30094.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6m5v_30094/08_2025/6m5v_30094.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6m5v_30094/08_2025/6m5v_30094.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6m5v_30094/08_2025/6m5v_30094.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6m5v_30094/08_2025/6m5v_30094.cif"
  }
  resolution = 4.5
  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=   0.001 sd=   0.015
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: 9
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P       2      5.49       5
     Mg      1      5.21       5
     S      47      5.16       5
     Be      1      3.05       5
     C    6703      2.51       5
     N    1893      2.21       5
     O    1897      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 86 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10549
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4482
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 585, 4482
          Classifications: {'peptide': 585}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 29, 'TRANS': 555}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 98
          Unresolved non-hydrogen angles: 124
          Unresolved non-hydrogen dihedrals: 77
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 5, 'ASP:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 84
    Chain: "B"
      Number of atoms: 5208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 670, 5208
          Classifications: {'peptide': 670}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 33, 'TRANS': 636}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "C"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 825
          Classifications: {'peptide': 104}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 99}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   5415  SG  CYS B 121      31.477  46.241  53.912  1.00 47.42           S
  ATOM  10277  SG  CYS C 101      30.191  46.342  57.304  1.00 59.52           S
  ATOM   6010  SG  CYS B 197      52.449  54.153  49.925  1.00 43.06           S
  ATOM   6028  SG  CYS B 200      54.145  55.532  52.620  1.00 41.30           S

  Time building chain proxies: 2.71, per 1000 atoms: 0.26
  Number of scatterers: 10549
  At special positions: 0
  Unit cell: (108.16, 101.92, 120.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 9
    Type Number    sf(0)
     Zn      2     29.99
     S      47     16.00
     P       2     15.00
     Mg      1     11.99
     F       3      9.00
     O    1897      8.00
     N    1893      7.00
     C    6703      6.00
     Be      1      4.00
    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: 1.13
  Conformation dependent library (CDL) restraints added in 440.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 801 "
        pdb="ZN    ZN B 801 " - pdb=" SG  CYS B 121 "
        pdb="ZN    ZN B 801 " - pdb=" SG  CYS C 101 "
      pdb="  ZN B 802 "
        pdb="ZN    ZN B 802 " - pdb=" SG  CYS B 200 "
        pdb="ZN    ZN B 802 " - pdb=" SG  CYS B 197 "


  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2566

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 7 sheets defined
      53.3% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 67 through 72
    Processing helix  chain 'A' and resid 73 through 81
      removed outlier: 4.300A  pdb=" N   VAL A  79 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 89
      removed outlier: 3.539A  pdb=" N   PHE A  85 " --> pdb=" O   ARG A  81 " (cutoff:3.500A)
      removed outlier: 4.817A  pdb=" N   SER A  87 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   LEU A  88 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL A  89 " --> pdb=" O   PHE A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 118
    Processing helix  chain 'A' and resid 129 through 149
      removed outlier: 3.731A  pdb=" N   GLN A 133 " --> pdb=" O   ASP A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 167
      removed outlier: 3.741A  pdb=" N   ASP A 162 " --> pdb=" O   HIS A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 170
      No H-bonds generated for 'chain 'A' and resid 168 through 170'
    Processing helix  chain 'A' and resid 203 through 221
      removed outlier: 4.173A  pdb=" N   LEU A 209 " --> pdb=" O   GLN A 205 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   PHE A 215 " --> pdb=" O   HIS A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 236
    Processing helix  chain 'A' and resid 242 through 250
      removed outlier: 3.673A  pdb=" N   VAL A 246 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.710A  pdb=" N   VAL A 269 " --> pdb=" O   THR A 265 " (cutoff:3.500A)
      Proline residue:  A 270  - end of helix
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 365 through 373
      removed outlier: 4.180A  pdb=" N   ILE A 369 " --> pdb=" O   ALA A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 489
    Processing helix  chain 'A' and resid 496 through 500
    Processing helix  chain 'A' and resid 549 through 569
    Processing helix  chain 'A' and resid 585 through 601
    Processing helix  chain 'A' and resid 639 through 653
    Processing helix  chain 'A' and resid 672 through 682
    Processing helix  chain 'A' and resid 706 through 719
    Processing helix  chain 'B' and resid 6 through 33
      removed outlier: 3.613A  pdb=" N   VAL B  10 " --> pdb=" O   SER B   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 41
    Processing helix  chain 'B' and resid 43 through 58
    Processing helix  chain 'B' and resid 61 through 70
    Processing helix  chain 'B' and resid 74 through 101
    Processing helix  chain 'B' and resid 106 through 115
      removed outlier: 3.598A  pdb=" N   PHE B 110 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 156
      removed outlier: 3.633A  pdb=" N   VAL B 146 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 180
      removed outlier: 3.818A  pdb=" N   PHE B 175 " --> pdb=" O   ARG B 171 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   GLY B 178 " --> pdb=" O   GLU B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 191
      removed outlier: 3.788A  pdb=" N   SER B 191 " --> pdb=" O   PRO B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 205
      removed outlier: 3.786A  pdb=" N   PHE B 201 " --> pdb=" O   CYS B 197 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLU B 202 " --> pdb=" O   ALA B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 217
    Processing helix  chain 'B' and resid 237 through 243
      removed outlier: 3.525A  pdb=" N   TYR B 242 " --> pdb=" O   GLU B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 265
    Processing helix  chain 'B' and resid 307 through 312
      removed outlier: 4.104A  pdb=" N   GLN B 312 " --> pdb=" O   SER B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 355
    Processing helix  chain 'B' and resid 374 through 381
      removed outlier: 3.764A  pdb=" N   ILE B 381 " --> pdb=" O   ASP B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 400
      removed outlier: 3.867A  pdb=" N   ALA B 398 " --> pdb=" O   ALA B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 414
    Processing helix  chain 'B' and resid 414 through 429
      removed outlier: 3.554A  pdb=" N   CYS B 418 " --> pdb=" O   SER B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 486 through 510
      removed outlier: 3.557A  pdb=" N   LEU B 502 " --> pdb=" O   GLU B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 511 through 531
      removed outlier: 3.542A  pdb=" N   MET B 529 " --> pdb=" O   GLU B 525 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 560
      removed outlier: 3.741A  pdb=" N   GLY B 549 " --> pdb=" O   ALA B 545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 574 through 587
      removed outlier: 3.936A  pdb=" N   ALA B 578 " --> pdb=" O   GLY B 574 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   PHE B 581 " --> pdb=" O   ASP B 577 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   MET B 582 " --> pdb=" O   ALA B 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 592 through 594
      No H-bonds generated for 'chain 'B' and resid 592 through 594'
    Processing helix  chain 'B' and resid 595 through 608
      removed outlier: 4.314A  pdb=" N   HIS B 601 " --> pdb=" O   PRO B 597 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   PHE B 604 " --> pdb=" O   THR B 600 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   LEU B 606 " --> pdb=" O   ARG B 602 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 622 through 633
      removed outlier: 3.912A  pdb=" N   SER B 630 " --> pdb=" O   ALA B 626 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 637 through 646
      removed outlier: 3.643A  pdb=" N   GLU B 642 " --> pdb=" O   PRO B 638 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   GLU B 643 " --> pdb=" O   HIS B 639 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU B 644 " --> pdb=" O   LEU B 640 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ALA B 645 " --> pdb=" O   LYS B 641 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 675 through 700
      removed outlier: 3.534A  pdb=" N   GLN B 679 " --> pdb=" O   ILE B 675 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 760 through 772
      removed outlier: 3.700A  pdb=" N   LEU B 769 " --> pdb=" O   LEU B 765 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 35
      removed outlier: 3.632A  pdb=" N   LEU C  30 " --> pdb=" O   THR C  26 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL C  35 " --> pdb=" O   ASP C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 80
      removed outlier: 3.627A  pdb=" N   LEU C  78 " --> pdb=" O   ARG C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 128
      removed outlier: 3.676A  pdb=" N   GLU C 105 " --> pdb=" O   CYS C 101 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA C 116 " --> pdb=" O   GLU C 112 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   HIS C 125 " --> pdb=" O   PHE C 121 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 59
    Processing sheet with id=AA2, first strand: chain 'A' and resid 381 through 386
      removed outlier: 7.623A  pdb=" N   THR A 254 " --> pdb=" O   PHE A 382 " (cutoff:3.500A)
      removed outlier: 7.710A  pdb=" N   SER A 384 " --> pdb=" O   THR A 254 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   PHE A 256 " --> pdb=" O   SER A 384 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   THR A 386 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   VAL A 258 " --> pdb=" O   THR A 386 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   VAL A 255 " --> pdb=" O   ASN A 408 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 287
    Processing sheet with id=AA4, first strand: chain 'A' and resid 314 through 316
      removed outlier: 3.656A  pdb=" N   SER A 332 " --> pdb=" O   PHE A 324 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 616 through 619
      removed outlier: 6.119A  pdb=" N   VAL A 576 " --> pdb=" O   LEU A 618 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   LEU A 504 " --> pdb=" O   ARG A 577 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   ALA A 579 " --> pdb=" O   LEU A 504 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   VAL A 506 " --> pdb=" O   ALA A 579 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   ASP A 503 " --> pdb=" O   ARG A 528 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   ARG A 528 " --> pdb=" O   ASP A 503 " (cutoff:3.500A)
      removed outlier: 5.581A  pdb=" N   THR A 521 " --> pdb=" O   HIS A 540 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   HIS A 540 " --> pdb=" O   THR A 521 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   VAL A 523 " --> pdb=" O   LEU A 538 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   LEU A 538 " --> pdb=" O   VAL A 523 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   VAL A 525 " --> pdb=" O   PHE A 536 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   TYR A 533 " --> pdb=" O   MET A 657 " (cutoff:3.500A)
      removed outlier: 7.266A  pdb=" N   SER A 659 " --> pdb=" O   TYR A 533 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   ILE A 535 " --> pdb=" O   SER A 659 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   GLU A 661 " --> pdb=" O   ILE A 535 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   ALA A 537 " --> pdb=" O   GLU A 661 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   VAL A 663 " --> pdb=" O   ALA A 537 " (cutoff:3.500A)
      removed outlier: 5.476A  pdb=" N   GLU A 539 " --> pdb=" O   VAL A 663 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 126
    Processing sheet with id=AA7, first strand: chain 'B' and resid 566 through 568
      removed outlier: 6.363A  pdb=" N   ILE B 567 " --> pdb=" O   TYR B 757 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   VAL B 738 " --> pdb=" O   TYR B 728 " (cutoff:3.500A)

    499 hydrogen bonds defined for protein.
    1452 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.74

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1691
        1.30 -     1.43: 2872
        1.43 -     1.56: 6132
        1.56 -     1.68: 13
        1.68 -     1.81: 68
  Bond restraints: 10776
  Sorted by residual:
  bond pdb=" F3  BEF A 802 "
       pdb="BE   BEF A 802 "
    ideal  model  delta    sigma   weight residual
    1.476  1.765 -0.289 2.00e-02 2.50e+03 2.09e+02
  bond pdb=" F1  BEF A 802 "
       pdb="BE   BEF A 802 "
    ideal  model  delta    sigma   weight residual
    1.476  1.765 -0.289 2.00e-02 2.50e+03 2.08e+02
  bond pdb=" F2  BEF A 802 "
       pdb="BE   BEF A 802 "
    ideal  model  delta    sigma   weight residual
    1.476  1.764 -0.288 2.00e-02 2.50e+03 2.08e+02
  bond pdb=" C   ALA A 482 "
       pdb=" O   ALA A 482 "
    ideal  model  delta    sigma   weight residual
    1.237  1.172  0.064 1.17e-02 7.31e+03 3.02e+01
  bond pdb=" C4  ADP A 801 "
       pdb=" C5  ADP A 801 "
    ideal  model  delta    sigma   weight residual
    1.490  1.380  0.110 2.00e-02 2.50e+03 3.01e+01
  ... (remaining 10771 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 14168
        2.17 -     4.34: 411
        4.34 -     6.50: 48
        6.50 -     8.67: 12
        8.67 -    10.84: 4
  Bond angle restraints: 14643
  Sorted by residual:
  angle pdb=" C   CYS A 125 "
        pdb=" N   ALA A 126 "
        pdb=" CA  ALA A 126 "
      ideal   model   delta    sigma   weight residual
     122.52  130.37   -7.85 1.16e+00 7.43e-01 4.58e+01
  angle pdb=" N   VAL A 477 "
        pdb=" CA  VAL A 477 "
        pdb=" C   VAL A 477 "
      ideal   model   delta    sigma   weight residual
     110.36  115.76   -5.40 1.05e+00 9.07e-01 2.64e+01
  angle pdb=" N   CYS A 125 "
        pdb=" CA  CYS A 125 "
        pdb=" C   CYS A 125 "
      ideal   model   delta    sigma   weight residual
     108.42  116.12   -7.70 1.54e+00 4.22e-01 2.50e+01
  angle pdb=" N   ARG B  59 "
        pdb=" CA  ARG B  59 "
        pdb=" C   ARG B  59 "
      ideal   model   delta    sigma   weight residual
     114.56  108.42    6.14 1.27e+00 6.20e-01 2.34e+01
  angle pdb=" N   SER A 481 "
        pdb=" CA  SER A 481 "
        pdb=" C   SER A 481 "
      ideal   model   delta    sigma   weight residual
     111.07  106.34    4.73 1.07e+00 8.73e-01 1.96e+01
  ... (remaining 14638 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.48: 5923
       23.48 -    46.95: 420
       46.95 -    70.43: 62
       70.43 -    93.91: 12
       93.91 -   117.38: 2
  Dihedral angle restraints: 6419
    sinusoidal: 2471
      harmonic: 3948
  Sorted by residual:
  dihedral pdb=" O2A ADP A 801 "
           pdb=" O3A ADP A 801 "
           pdb=" PA  ADP A 801 "
           pdb=" PB  ADP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   57.38 -117.38     1      2.00e+01 2.50e-03 3.50e+01
  dihedral pdb=" CA  CYS B 223 "
           pdb=" C   CYS B 223 "
           pdb=" N   ASN B 224 "
           pdb=" CA  ASN B 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.99   27.01     0      5.00e+00 4.00e-02 2.92e+01
  dihedral pdb=" C5' ADP A 801 "
           pdb=" O5' ADP A 801 "
           pdb=" PA  ADP A 801 "
           pdb=" O2A ADP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   37.46  -97.45     1      2.00e+01 2.50e-03 2.71e+01
  ... (remaining 6416 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1469
       0.073 -    0.146: 184
       0.146 -    0.219: 22
       0.219 -    0.292: 5
       0.292 -    0.365: 1
  Chirality restraints: 1681
  Sorted by residual:
  chirality pdb=" CA  VAL A 558 "
            pdb=" N   VAL A 558 "
            pdb=" C   VAL A 558 "
            pdb=" CB  VAL A 558 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.08    0.37 2.00e-01 2.50e+01 3.34e+00
  chirality pdb=" CA  HIS B 535 "
            pdb=" N   HIS B 535 "
            pdb=" C   HIS B 535 "
            pdb=" CB  HIS B 535 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.90e+00
  chirality pdb=" CA  VAL A 663 "
            pdb=" N   VAL A 663 "
            pdb=" C   VAL A 663 "
            pdb=" CB  VAL A 663 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.70   -0.26 2.00e-01 2.50e+01 1.73e+00
  ... (remaining 1678 not shown)

  Planarity restraints: 1892
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 242 "   -0.016 2.00e-02 2.50e+03   3.26e-02 1.06e+01
        pdb=" C   TYR B 242 "    0.056 2.00e-02 2.50e+03
        pdb=" O   TYR B 242 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LEU B 243 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 534 "    0.013 2.00e-02 2.50e+03   2.56e-02 6.54e+00
        pdb=" C   VAL B 534 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   VAL B 534 "    0.016 2.00e-02 2.50e+03
        pdb=" N   HIS B 535 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 724 "    0.036 5.00e-02 4.00e+02   5.48e-02 4.81e+00
        pdb=" N   PRO A 725 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 725 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 725 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1889 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1375
        2.75 -     3.29: 10606
        3.29 -     3.82: 17403
        3.82 -     4.36: 20209
        4.36 -     4.90: 34871
  Nonbonded interactions: 84464
  Sorted by model distance:
  nonbonded pdb=" O   CYS B 223 "
            pdb=" ND1 HIS B 225 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" O   CYS C 101 "
            pdb=" N   GLY C 104 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" NE2 HIS B 157 "
            pdb=" O   ASN B 608 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" O   SER B 713 "
            pdb=" OG  SER B 713 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   GLY A 654 "
            pdb=" NH1 ARG C 120 "
     model   vdw
     2.281 3.120
  ... (remaining 84459 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             0.390
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.860
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5902
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.640  10780  Z= 0.469
  Angle     :  0.865  10.839  14643  Z= 0.538
  Chirality :  0.051   0.365   1681
  Planarity :  0.005   0.055   1892
  Dihedral  : 16.072 117.384   3853
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 18.28
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.95 %
    Favored  : 90.90 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 16.77 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.04 (0.21), residues: 1329
  helix: -1.01 (0.18), residues: 692
  sheet: -1.77 (0.52), residues: 92
  loop : -3.41 (0.23), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 528 
 TYR   0.019   0.002   TYR A 507 
 PHE   0.023   0.002   PHE A 634 
 TRP   0.012   0.002   TRP A 308 
 HIS   0.009   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00746 (10776)
  covalent geometry    : angle       0.86451 (14643)
  hydrogen bonds       : bond        0.13155 (  499)
  hydrogen bonds       : angle       5.74740 ( 1452)
  metal coordination   : bond        0.32804 (    4)

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

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

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 272
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 PHE cc_start: 0.6916 (t80) cc_final: 0.6557 (t80)
REVERT: A   84 LEU cc_start: 0.8467 (tp) cc_final: 0.8061 (tp)
REVERT: A   93 LEU cc_start: 0.8718 (mt) cc_final: 0.8170 (tt)
REVERT: A  203 LEU cc_start: 0.8736 (tp) cc_final: 0.8425 (tp)
REVERT: A  210 MET cc_start: 0.8690 (mtm) cc_final: 0.8197 (ttm)
REVERT: A  213 THR cc_start: 0.8188 (m) cc_final: 0.7815 (p)
REVERT: A  241 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8679 (m-80)
REVERT: A  249 PHE cc_start: 0.7879 (m-10) cc_final: 0.7323 (m-10)
REVERT: A  271 LEU cc_start: 0.7751 (tt) cc_final: 0.7409 (tt)
REVERT: A  600 MET cc_start: 0.6732 (mmp) cc_final: 0.6011 (tpt)
REVERT: B   49 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.6350 (mt)
REVERT: B  143 LEU cc_start: 0.7896 (mt) cc_final: 0.7646 (mt)
REVERT: B  156 CYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8210 (m)
REVERT: B  601 HIS cc_start: 0.8142 (m-70) cc_final: 0.7790 (m170)
REVERT: B  690 ILE cc_start: 0.7997 (mt) cc_final: 0.7684 (tp)
REVERT: B  748 CYS cc_start: 0.4796 (OUTLIER) cc_final: 0.4148 (t)
REVERT: B  766 TYR cc_start: 0.6760 (t80) cc_final: 0.6452 (t80)
REVERT: C   42 ASP cc_start: 0.6139 (t0) cc_final: 0.5889 (t0)
REVERT: C   63 ASP cc_start: 0.8344 (m-30) cc_final: 0.7710 (m-30)
REVERT: C   77 SER cc_start: 0.8905 (m) cc_final: 0.8335 (p)
REVERT: C   79 LEU cc_start: 0.8452 (mt) cc_final: 0.8160 (tp)
  outliers start: 60
  outliers final: 11
  residues processed: 319
  average time/residue: 0.1515
  time to fit residues: 62.6071
Evaluate side-chains
  171 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 156
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:   40.0000
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:   20.0000
   chunk 55 optimal weight:    8.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  67 HIS
A 102 HIS
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 148 HIS
A 224 HIS
** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 GLN
A 377 ASN
A 670 GLN
A 726 HIS
B  68 GLN
** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 GLN
B 144 HIS
B 195 HIS
B 210 GLN
B 323 GLN
B 342 GLN
B 491 GLN
B 614 HIS
** B 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 119 ASN
C 126 GLN

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.086951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.071450 restraints weight = 56808.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.073203 restraints weight = 40296.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.074494 restraints weight = 30624.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.075435 restraints weight = 24563.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.076183 restraints weight = 20579.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.3690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10780  Z= 0.179
  Angle     :  0.740   9.649  14643  Z= 0.372
  Chirality :  0.044   0.207   1681
  Planarity :  0.006   0.067   1892
  Dihedral  :  6.782 129.771   1501
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 16.32
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.50 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  4.22 %
    Favored  : 95.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.71 (0.23), residues: 1329
  helix:  0.04 (0.20), residues: 695
  sheet: -1.84 (0.48), residues: 103
  loop : -2.59 (0.27), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  93 
 TYR   0.024   0.002   TYR B 123 
 PHE   0.030   0.002   PHE A 241 
 TRP   0.039   0.002   TRP A 308 
 HIS   0.012   0.001   HIS B 617 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (10776)
  covalent geometry    : angle       0.73960 (14643)
  hydrogen bonds       : bond        0.03931 (  499)
  hydrogen bonds       : angle       4.28389 ( 1452)
  metal coordination   : bond        0.00512 (    4)

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

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

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 181
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 PHE cc_start: 0.8757 (t80) cc_final: 0.8169 (t80)
REVERT: A   94 LYS cc_start: 0.8579 (mmtt) cc_final: 0.8277 (mmmt)
REVERT: A  201 LEU cc_start: 0.9374 (mt) cc_final: 0.9171 (mt)
REVERT: A  204 PHE cc_start: 0.8929 (p90) cc_final: 0.8470 (p90)
REVERT: A  205 GLN cc_start: 0.8583 (mt0) cc_final: 0.8324 (mm-40)
REVERT: A  206 LYS cc_start: 0.8259 (mtpt) cc_final: 0.7736 (mmmm)
REVERT: A  207 MET cc_start: 0.8418 (mtp) cc_final: 0.8151 (mtm)
REVERT: A  213 THR cc_start: 0.8938 (m) cc_final: 0.8615 (p)
REVERT: A  216 LEU cc_start: 0.8846 (mt) cc_final: 0.8477 (mt)
REVERT: A  284 ILE cc_start: 0.9139 (mt) cc_final: 0.8559 (mp)
REVERT: A  299 GLU cc_start: 0.8902 (tp30) cc_final: 0.8529 (tp30)
REVERT: A  335 VAL cc_start: 0.9414 (m) cc_final: 0.9021 (p)
REVERT: A  500 MET cc_start: 0.2267 (mpp) cc_final: 0.1429 (mpp)
REVERT: A  600 MET cc_start: 0.8741 (mmp) cc_final: 0.8080 (tpt)
REVERT: B   28 GLN cc_start: 0.9361 (mm-40) cc_final: 0.9028 (mm-40)
REVERT: B  115 MET cc_start: 0.7082 (mmm) cc_final: 0.6314 (mmp)
REVERT: B  232 VAL cc_start: 0.9004 (p) cc_final: 0.8526 (p)
REVERT: B  326 MET cc_start: 0.6858 (tpp) cc_final: 0.6598 (tpt)
REVERT: B  375 MET cc_start: 0.6233 (mmm) cc_final: 0.6005 (mmm)
REVERT: B  419 ASP cc_start: 0.8570 (p0) cc_final: 0.8093 (p0)
REVERT: C   60 PRO cc_start: 0.8755 (Cg_endo) cc_final: 0.8198 (Cg_exo)
REVERT: C   63 ASP cc_start: 0.8587 (m-30) cc_final: 0.8052 (m-30)
  outliers start: 2
  outliers final: 1
  residues processed: 183
  average time/residue: 0.1250
  time to fit residues: 31.1769
Evaluate side-chains
  124 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 72 optimal weight:    9.9990
   chunk 32 optimal weight:   30.0000
   chunk 6 optimal weight:   20.0000
   chunk 61 optimal weight:    6.9990
   chunk 34 optimal weight:    8.9990
   chunk 127 optimal weight:    8.9990
   chunk 52 optimal weight:    7.9990
   chunk 126 optimal weight:    3.9990
   chunk 14 optimal weight:    8.9990
   chunk 120 optimal weight:   30.0000
   chunk 11 optimal weight:    5.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 HIS
A 374 ASN
** B  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 137 HIS
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 GLN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  67 ASN
C 119 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.079897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.065454 restraints weight = 61384.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.067019 restraints weight = 43488.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.068169 restraints weight = 33159.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.069036 restraints weight = 26698.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.069597 restraints weight = 22453.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.5182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.082  10780  Z= 0.260
  Angle     :  0.806  11.153  14643  Z= 0.412
  Chirality :  0.045   0.168   1681
  Planarity :  0.008   0.222   1892
  Dihedral  :  6.687 132.834   1501
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 21.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.33 %
    Favored  : 90.67 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  5.59 %
    Favored  : 94.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.20 (0.23), residues: 1329
  helix:  0.48 (0.20), residues: 687
  sheet: -1.53 (0.49), residues: 99
  loop : -2.38 (0.27), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C  71 
 TYR   0.018   0.002   TYR B 721 
 PHE   0.025   0.003   PHE A 633 
 TRP   0.030   0.003   TRP A 308 
 HIS   0.011   0.002   HIS B 617 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 (10776)
  covalent geometry    : angle       0.80621 (14643)
  hydrogen bonds       : bond        0.04100 (  499)
  hydrogen bonds       : angle       4.45506 ( 1452)
  metal coordination   : bond        0.00645 (    4)

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

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

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 149
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.8587 (mmtt) cc_final: 0.8184 (mmmt)
REVERT: A  203 LEU cc_start: 0.9115 (tp) cc_final: 0.8835 (tp)
REVERT: A  206 LYS cc_start: 0.7975 (mtpt) cc_final: 0.7202 (mmmm)
REVERT: A  207 MET cc_start: 0.8652 (mtp) cc_final: 0.7991 (mtp)
REVERT: A  210 MET cc_start: 0.9113 (mtm) cc_final: 0.8895 (mtp)
REVERT: A  262 HIS cc_start: 0.9531 (m90) cc_final: 0.9296 (m170)
REVERT: A  324 PHE cc_start: 0.6559 (t80) cc_final: 0.6281 (t80)
REVERT: A  500 MET cc_start: 0.3497 (mpp) cc_final: 0.2241 (mpp)
REVERT: A  600 MET cc_start: 0.8834 (mmp) cc_final: 0.8100 (tpt)
REVERT: B  232 VAL cc_start: 0.8724 (p) cc_final: 0.8305 (p)
REVERT: B  419 ASP cc_start: 0.8605 (p0) cc_final: 0.8343 (p0)
REVERT: B  687 ARG cc_start: 0.9062 (ttp80) cc_final: 0.8766 (ttp80)
REVERT: B  704 GLU cc_start: 0.9341 (pm20) cc_final: 0.8954 (pm20)
REVERT: B  737 LEU cc_start: 0.8015 (mt) cc_final: 0.7732 (mt)
REVERT: C   50 MET cc_start: 0.8325 (ttm) cc_final: 0.6798 (mmm)
REVERT: C   63 ASP cc_start: 0.8133 (m-30) cc_final: 0.7484 (m-30)
  outliers start: 2
  outliers final: 2
  residues processed: 151
  average time/residue: 0.1174
  time to fit residues: 25.0075
Evaluate side-chains
  111 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 109
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 92 optimal weight:   10.0000
   chunk 134 optimal weight:    9.9990
   chunk 94 optimal weight:    9.9990
   chunk 112 optimal weight:    8.9990
   chunk 31 optimal weight:    6.9990
   chunk 38 optimal weight:    9.9990
   chunk 101 optimal weight:    7.9990
   chunk 129 optimal weight:    8.9990
   chunk 27 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    4.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  13 GLN
B  50 ASN
** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 GLN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  67 ASN
C  73 GLN
C 119 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.080232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.065578 restraints weight = 60891.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.067186 restraints weight = 42879.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.068400 restraints weight = 32468.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.069301 restraints weight = 25995.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.069859 restraints weight = 21699.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.5685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10780  Z= 0.187
  Angle     :  0.731   9.913  14643  Z= 0.369
  Chirality :  0.043   0.156   1681
  Planarity :  0.006   0.049   1892
  Dihedral  :  6.593 138.884   1501
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 17.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.02 (0.23), residues: 1329
  helix:  0.55 (0.20), residues: 697
  sheet: -1.62 (0.51), residues: 88
  loop : -2.18 (0.27), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  60 
 TYR   0.018   0.002   TYR B 728 
 PHE   0.023   0.002   PHE B 543 
 TRP   0.052   0.002   TRP A 308 
 HIS   0.008   0.001   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (10776)
  covalent geometry    : angle       0.73135 (14643)
  hydrogen bonds       : bond        0.03755 (  499)
  hydrogen bonds       : angle       4.32622 ( 1452)
  metal coordination   : bond        0.00366 (    4)

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

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

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.8421 (mmtt) cc_final: 0.7778 (mmmt)
REVERT: A  202 GLU cc_start: 0.8786 (tp30) cc_final: 0.8068 (tm-30)
REVERT: A  210 MET cc_start: 0.9077 (mtm) cc_final: 0.8541 (mtp)
REVERT: A  216 LEU cc_start: 0.8651 (mt) cc_final: 0.8422 (mt)
REVERT: A  262 HIS cc_start: 0.9495 (m90) cc_final: 0.9146 (m90)
REVERT: A  283 LYS cc_start: 0.9109 (mmtm) cc_final: 0.8460 (mmmt)
REVERT: A  299 GLU cc_start: 0.9019 (tp30) cc_final: 0.8774 (tp30)
REVERT: A  324 PHE cc_start: 0.6619 (t80) cc_final: 0.6370 (t80)
REVERT: A  500 MET cc_start: 0.3749 (mpp) cc_final: 0.2349 (mpp)
REVERT: A  600 MET cc_start: 0.8261 (mmp) cc_final: 0.7648 (tpt)
REVERT: B  419 ASP cc_start: 0.8570 (p0) cc_final: 0.8132 (p0)
REVERT: B  695 LEU cc_start: 0.9523 (mm) cc_final: 0.9164 (mm)
REVERT: B  704 GLU cc_start: 0.9368 (pm20) cc_final: 0.8963 (pm20)
REVERT: B  737 LEU cc_start: 0.7715 (mt) cc_final: 0.7264 (mt)
REVERT: C   63 ASP cc_start: 0.8103 (m-30) cc_final: 0.7630 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1221
  time to fit residues: 23.8897
Evaluate side-chains
  106 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 134 optimal weight:    1.9990
   chunk 91 optimal weight:   20.0000
   chunk 100 optimal weight:    5.9990
   chunk 122 optimal weight:    7.9990
   chunk 40 optimal weight:    7.9990
   chunk 113 optimal weight:    8.9990
   chunk 61 optimal weight:    8.9990
   chunk 96 optimal weight:    6.9990
   chunk 44 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 48 optimal weight:    8.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 229 GLN
** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 GLN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 617 HIS
B 621 GLN
B 771 HIS
C  67 ASN
** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 119 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.079280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.065267 restraints weight = 61778.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.066921 restraints weight = 42979.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.068134 restraints weight = 32188.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.069008 restraints weight = 25447.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.069672 restraints weight = 21079.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.6154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10780  Z= 0.192
  Angle     :  0.725  10.586  14643  Z= 0.365
  Chirality :  0.042   0.156   1681
  Planarity :  0.005   0.048   1892
  Dihedral  :  6.507 134.542   1501
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 18.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.65 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.31 %
    Favored  : 95.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.87 (0.24), residues: 1329
  helix:  0.66 (0.20), residues: 695
  sheet: -1.64 (0.52), residues: 88
  loop : -2.05 (0.28), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  60 
 TYR   0.019   0.002   TYR A 397 
 PHE   0.024   0.002   PHE B 556 
 TRP   0.035   0.002   TRP A 308 
 HIS   0.015   0.002   HIS B 617 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 (10776)
  covalent geometry    : angle       0.72507 (14643)
  hydrogen bonds       : bond        0.03671 (  499)
  hydrogen bonds       : angle       4.42646 ( 1452)
  metal coordination   : bond        0.00439 (    4)

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

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

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7617 (mmmt)
REVERT: A  210 MET cc_start: 0.9087 (mtm) cc_final: 0.8724 (mtt)
REVERT: A  262 HIS cc_start: 0.9556 (m90) cc_final: 0.9261 (m90)
REVERT: A  299 GLU cc_start: 0.8855 (tp30) cc_final: 0.8581 (tp30)
REVERT: A  324 PHE cc_start: 0.6480 (t80) cc_final: 0.6222 (t80)
REVERT: A  352 LEU cc_start: 0.9059 (mt) cc_final: 0.8776 (mt)
REVERT: A  500 MET cc_start: 0.3962 (mpp) cc_final: 0.2570 (mpp)
REVERT: A  600 MET cc_start: 0.8299 (mmp) cc_final: 0.7624 (tpt)
REVERT: B  419 ASP cc_start: 0.8700 (p0) cc_final: 0.8260 (p0)
REVERT: B  690 ILE cc_start: 0.9411 (pt) cc_final: 0.9091 (tp)
REVERT: B  695 LEU cc_start: 0.9542 (mm) cc_final: 0.9135 (mm)
REVERT: B  704 GLU cc_start: 0.9468 (pm20) cc_final: 0.8998 (pm20)
REVERT: B  737 LEU cc_start: 0.7608 (mt) cc_final: 0.7296 (mt)
REVERT: C   50 MET cc_start: 0.7834 (mtt) cc_final: 0.7210 (mmp)
REVERT: C   60 PRO cc_start: 0.8233 (Cg_endo) cc_final: 0.8003 (Cg_exo)
REVERT: C   63 ASP cc_start: 0.8128 (m-30) cc_final: 0.7651 (m-30)
  outliers start: 1
  outliers final: 1
  residues processed: 128
  average time/residue: 0.1259
  time to fit residues: 22.3677
Evaluate side-chains
  99 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 96 optimal weight:   20.0000
   chunk 110 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 101 optimal weight:    5.9990
   chunk 48 optimal weight:    7.9990
   chunk 127 optimal weight:   20.0000
   chunk 102 optimal weight:    6.9990
   chunk 29 optimal weight:   20.0000
   chunk 128 optimal weight:    7.9990
   chunk 59 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    3.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 597 HIS
** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 GLN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  67 ASN
** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 119 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.079115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.065105 restraints weight = 61297.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.066790 restraints weight = 42308.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.068001 restraints weight = 31467.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.068823 restraints weight = 24841.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.069528 restraints weight = 20700.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.6476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10780  Z= 0.170
  Angle     :  0.713  10.950  14643  Z= 0.356
  Chirality :  0.042   0.239   1681
  Planarity :  0.005   0.047   1892
  Dihedral  :  6.410 134.528   1501
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 18.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.73 (0.24), residues: 1329
  helix:  0.76 (0.20), residues: 696
  sheet: -1.59 (0.54), residues: 88
  loop : -1.97 (0.29), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  60 
 TYR   0.017   0.002   TYR B 728 
 PHE   0.026   0.002   PHE B 556 
 TRP   0.032   0.002   TRP A 308 
 HIS   0.012   0.001   HIS B 617 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (10776)
  covalent geometry    : angle       0.71302 (14643)
  hydrogen bonds       : bond        0.03597 (  499)
  hydrogen bonds       : angle       4.33793 ( 1452)
  metal coordination   : bond        0.00293 (    4)

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

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

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7742 (mmmt)
REVERT: A  201 LEU cc_start: 0.8921 (mt) cc_final: 0.8056 (mt)
REVERT: A  202 GLU cc_start: 0.8452 (tp30) cc_final: 0.7950 (tm-30)
REVERT: A  203 LEU cc_start: 0.8924 (tp) cc_final: 0.8571 (tp)
REVERT: A  210 MET cc_start: 0.9261 (mtm) cc_final: 0.8719 (ttm)
REVERT: A  262 HIS cc_start: 0.9554 (m90) cc_final: 0.9236 (m90)
REVERT: A  299 GLU cc_start: 0.8886 (tp30) cc_final: 0.8586 (tp30)
REVERT: A  324 PHE cc_start: 0.6585 (t80) cc_final: 0.6346 (t80)
REVERT: A  352 LEU cc_start: 0.9255 (mt) cc_final: 0.9006 (mt)
REVERT: A  500 MET cc_start: 0.2929 (mpp) cc_final: 0.2655 (mpp)
REVERT: A  600 MET cc_start: 0.8336 (mmp) cc_final: 0.7837 (tpt)
REVERT: B  390 ASP cc_start: 0.9637 (t0) cc_final: 0.9138 (t0)
REVERT: B  419 ASP cc_start: 0.8669 (p0) cc_final: 0.8146 (p0)
REVERT: B  523 ARG cc_start: 0.9116 (ppt170) cc_final: 0.8252 (ttp80)
REVERT: B  695 LEU cc_start: 0.9529 (mm) cc_final: 0.9125 (mm)
REVERT: B  704 GLU cc_start: 0.9475 (pm20) cc_final: 0.8986 (pm20)
REVERT: B  737 LEU cc_start: 0.7563 (mt) cc_final: 0.7209 (mt)
REVERT: C   15 ASP cc_start: 0.8349 (t0) cc_final: 0.7985 (t0)
REVERT: C   50 MET cc_start: 0.8141 (mtt) cc_final: 0.6963 (mmt)
REVERT: C   54 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8141 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1206
  time to fit residues: 21.6628
Evaluate side-chains
  105 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 57 optimal weight:   20.0000
   chunk 113 optimal weight:    7.9990
   chunk 28 optimal weight:    9.9990
   chunk 134 optimal weight:   10.0000
   chunk 103 optimal weight:   20.0000
   chunk 108 optimal weight:    6.9990
   chunk 94 optimal weight:    9.9990
   chunk 117 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 12 optimal weight:    0.0020
   chunk 45 optimal weight:   40.0000
   overall best weight:    6.9996

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 646 HIS
** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  67 ASN
** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 119 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.075078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.061850 restraints weight = 63101.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.063353 restraints weight = 44192.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.064452 restraints weight = 33295.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.065177 restraints weight = 26550.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.065800 restraints weight = 22372.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.7255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  10780  Z= 0.252
  Angle     :  0.804  10.455  14643  Z= 0.411
  Chirality :  0.044   0.181   1681
  Planarity :  0.006   0.066   1892
  Dihedral  :  6.664 133.495   1501
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 23.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.93 %
    Favored  : 90.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (0.24), residues: 1329
  helix:  0.44 (0.19), residues: 697
  sheet: -1.78 (0.51), residues: 96
  loop : -2.06 (0.29), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 709 
 TYR   0.022   0.002   TYR A 397 
 PHE   0.024   0.003   PHE A 159 
 TRP   0.055   0.004   TRP A 308 
 HIS   0.019   0.002   HIS B 617 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 (10776)
  covalent geometry    : angle       0.80354 (14643)
  hydrogen bonds       : bond        0.04082 (  499)
  hydrogen bonds       : angle       4.70265 ( 1452)
  metal coordination   : bond        0.00308 (    4)

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

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

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8201 (mmmt)
REVERT: A  122 PHE cc_start: 0.8246 (m-80) cc_final: 0.7419 (m-80)
REVERT: A  201 LEU cc_start: 0.8951 (mt) cc_final: 0.8450 (mt)
REVERT: A  202 GLU cc_start: 0.8665 (tp30) cc_final: 0.7949 (tm-30)
REVERT: A  203 LEU cc_start: 0.8867 (tp) cc_final: 0.8537 (tp)
REVERT: A  210 MET cc_start: 0.9306 (mtm) cc_final: 0.8533 (ttm)
REVERT: A  249 PHE cc_start: 0.8656 (m-80) cc_final: 0.8112 (m-80)
REVERT: A  262 HIS cc_start: 0.9612 (m90) cc_final: 0.9360 (m90)
REVERT: A  280 ARG cc_start: 0.6891 (mmm-85) cc_final: 0.6197 (mmm-85)
REVERT: A  299 GLU cc_start: 0.9057 (tp30) cc_final: 0.8637 (tp30)
REVERT: A  324 PHE cc_start: 0.6873 (t80) cc_final: 0.6626 (t80)
REVERT: A  352 LEU cc_start: 0.9280 (mt) cc_final: 0.9032 (mt)
REVERT: A  500 MET cc_start: 0.4626 (mpp) cc_final: 0.4119 (mpp)
REVERT: A  600 MET cc_start: 0.8449 (mmp) cc_final: 0.7774 (tpt)
REVERT: B  419 ASP cc_start: 0.8394 (p0) cc_final: 0.7705 (p0)
REVERT: B  523 ARG cc_start: 0.9239 (ppt170) cc_final: 0.8976 (ttt-90)
REVERT: B  657 ASP cc_start: 0.8323 (m-30) cc_final: 0.7794 (t0)
REVERT: B  695 LEU cc_start: 0.9500 (mm) cc_final: 0.9264 (mm)
REVERT: B  704 GLU cc_start: 0.9407 (pm20) cc_final: 0.8968 (pm20)
REVERT: C   15 ASP cc_start: 0.8395 (t0) cc_final: 0.8181 (t70)
REVERT: C   50 MET cc_start: 0.8263 (mtt) cc_final: 0.6824 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1292
  time to fit residues: 22.4374
Evaluate side-chains
  97 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 76 optimal weight:    0.9980
   chunk 123 optimal weight:    9.9990
   chunk 129 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 95 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 83 optimal weight:    8.9990
   chunk 46 optimal weight:   30.0000
   chunk 113 optimal weight:    0.4980
   chunk 44 optimal weight:    6.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 GLN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  25 GLN
C  67 ASN
** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 119 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.078883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.064947 restraints weight = 60296.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.066622 restraints weight = 41779.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.067826 restraints weight = 31009.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.068714 restraints weight = 24439.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.069308 restraints weight = 20198.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.7233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  10780  Z= 0.139
  Angle     :  0.724  12.462  14643  Z= 0.357
  Chirality :  0.043   0.173   1681
  Planarity :  0.005   0.046   1892
  Dihedral  :  6.418 131.628   1501
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 16.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.65 (0.24), residues: 1329
  helix:  0.80 (0.20), residues: 704
  sheet: -1.77 (0.54), residues: 86
  loop : -1.87 (0.29), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  33 
 TYR   0.017   0.001   TYR A 138 
 PHE   0.022   0.002   PHE B 329 
 TRP   0.052   0.002   TRP A 308 
 HIS   0.009   0.001   HIS B 617 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (10776)
  covalent geometry    : angle       0.72387 (14643)
  hydrogen bonds       : bond        0.03498 (  499)
  hydrogen bonds       : angle       4.41575 ( 1452)
  metal coordination   : bond        0.00182 (    4)

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

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

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.8360 (mmtt) cc_final: 0.7983 (mmmt)
REVERT: A  122 PHE cc_start: 0.8025 (m-80) cc_final: 0.7325 (m-80)
REVERT: A  201 LEU cc_start: 0.8864 (mt) cc_final: 0.8652 (mt)
REVERT: A  202 GLU cc_start: 0.8506 (tp30) cc_final: 0.7742 (tm-30)
REVERT: A  203 LEU cc_start: 0.8840 (tp) cc_final: 0.8349 (tp)
REVERT: A  210 MET cc_start: 0.9367 (mtm) cc_final: 0.8182 (ttm)
REVERT: A  262 HIS cc_start: 0.9448 (m90) cc_final: 0.9233 (m90)
REVERT: A  280 ARG cc_start: 0.7120 (mmm-85) cc_final: 0.6227 (mmm-85)
REVERT: A  283 LYS cc_start: 0.9191 (mmtm) cc_final: 0.8681 (mmpt)
REVERT: A  299 GLU cc_start: 0.9167 (tp30) cc_final: 0.8691 (tp30)
REVERT: A  324 PHE cc_start: 0.7394 (t80) cc_final: 0.6678 (t80)
REVERT: A  352 LEU cc_start: 0.9276 (mt) cc_final: 0.9046 (mt)
REVERT: A  370 MET cc_start: 0.7203 (mmp) cc_final: 0.6925 (mmm)
REVERT: A  600 MET cc_start: 0.8417 (mmp) cc_final: 0.7721 (tpt)
REVERT: B  155 TYR cc_start: 0.8300 (t80) cc_final: 0.7829 (t80)
REVERT: B  390 ASP cc_start: 0.9538 (t0) cc_final: 0.9102 (t0)
REVERT: B  419 ASP cc_start: 0.8270 (p0) cc_final: 0.7689 (p0)
REVERT: B  523 ARG cc_start: 0.9224 (ppt170) cc_final: 0.8270 (ttp80)
REVERT: B  657 ASP cc_start: 0.8166 (m-30) cc_final: 0.7662 (t0)
REVERT: B  695 LEU cc_start: 0.9488 (mm) cc_final: 0.9167 (mm)
REVERT: B  704 GLU cc_start: 0.9410 (pm20) cc_final: 0.9048 (pm20)
REVERT: B  737 LEU cc_start: 0.7577 (mt) cc_final: 0.7212 (mt)
REVERT: C   45 VAL cc_start: 0.6790 (t) cc_final: 0.6248 (t)
REVERT: C   50 MET cc_start: 0.8097 (mtt) cc_final: 0.6808 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1155
  time to fit residues: 22.9070
Evaluate side-chains
  103 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 77 optimal weight:    9.9990
   chunk 55 optimal weight:    9.9990
   chunk 133 optimal weight:    9.9990
   chunk 68 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0370
   chunk 107 optimal weight:    0.5980
   chunk 117 optimal weight:    9.9990
   chunk 106 optimal weight:    6.9990
   chunk 40 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    2.1264

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 GLN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  67 ASN
C 119 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.078257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.064896 restraints weight = 60114.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.066340 restraints weight = 42932.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.067442 restraints weight = 32779.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.068255 restraints weight = 26338.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.068826 restraints weight = 22051.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.7350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10780  Z= 0.142
  Angle     :  0.716  13.962  14643  Z= 0.353
  Chirality :  0.043   0.294   1681
  Planarity :  0.005   0.044   1892
  Dihedral  :  6.297 131.252   1501
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 17.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.24), residues: 1329
  helix:  0.87 (0.20), residues: 701
  sheet: -1.59 (0.51), residues: 96
  loop : -1.81 (0.30), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 570 
 TYR   0.016   0.001   TYR A 286 
 PHE   0.055   0.002   PHE A 241 
 TRP   0.048   0.003   TRP A 308 
 HIS   0.008   0.001   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (10776)
  covalent geometry    : angle       0.71634 (14643)
  hydrogen bonds       : bond        0.03478 (  499)
  hydrogen bonds       : angle       4.35659 ( 1452)
  metal coordination   : bond        0.00164 (    4)

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

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

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.8340 (mmtt) cc_final: 0.8009 (mmmt)
REVERT: A  122 PHE cc_start: 0.8007 (m-80) cc_final: 0.7277 (m-80)
REVERT: A  201 LEU cc_start: 0.9208 (mt) cc_final: 0.8504 (mt)
REVERT: A  202 GLU cc_start: 0.8443 (tp30) cc_final: 0.7900 (tm-30)
REVERT: A  203 LEU cc_start: 0.8778 (tp) cc_final: 0.8553 (tt)
REVERT: A  210 MET cc_start: 0.9226 (mtm) cc_final: 0.8008 (ttm)
REVERT: A  262 HIS cc_start: 0.9437 (m90) cc_final: 0.9221 (m90)
REVERT: A  280 ARG cc_start: 0.7068 (mmm-85) cc_final: 0.6181 (mmm-85)
REVERT: A  283 LYS cc_start: 0.9149 (mmtm) cc_final: 0.8669 (mmpt)
REVERT: A  299 GLU cc_start: 0.9209 (tp30) cc_final: 0.8765 (tp30)
REVERT: A  324 PHE cc_start: 0.7258 (t80) cc_final: 0.6966 (t80)
REVERT: A  352 LEU cc_start: 0.9289 (mt) cc_final: 0.9049 (mt)
REVERT: A  370 MET cc_start: 0.7123 (mmp) cc_final: 0.6890 (mmm)
REVERT: A  600 MET cc_start: 0.8441 (mmp) cc_final: 0.7776 (tpt)
REVERT: B  155 TYR cc_start: 0.8330 (t80) cc_final: 0.7866 (t80)
REVERT: B  390 ASP cc_start: 0.9500 (t0) cc_final: 0.9120 (t0)
REVERT: B  419 ASP cc_start: 0.8213 (p0) cc_final: 0.7570 (p0)
REVERT: B  523 ARG cc_start: 0.9223 (ppt170) cc_final: 0.8231 (ttp80)
REVERT: B  695 LEU cc_start: 0.9477 (mm) cc_final: 0.9159 (mm)
REVERT: B  704 GLU cc_start: 0.9436 (pm20) cc_final: 0.9023 (pm20)
REVERT: B  737 LEU cc_start: 0.7631 (mt) cc_final: 0.7273 (mt)
REVERT: C   45 VAL cc_start: 0.6663 (t) cc_final: 0.6079 (t)
REVERT: C   50 MET cc_start: 0.8007 (mtt) cc_final: 0.6731 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1057
  time to fit residues: 19.0892
Evaluate side-chains
  97 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 68 optimal weight:    7.9990
   chunk 105 optimal weight:    0.6980
   chunk 128 optimal weight:    9.9990
   chunk 41 optimal weight:   40.0000
   chunk 28 optimal weight:    5.9990
   chunk 77 optimal weight:    6.9990
   chunk 130 optimal weight:    9.9990
   chunk 9 optimal weight:    1.9990
   chunk 15 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    3.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 GLN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  67 ASN
C 119 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.077292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.064128 restraints weight = 61453.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.065531 restraints weight = 43477.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.066609 restraints weight = 33202.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.067413 restraints weight = 26679.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.068009 restraints weight = 22373.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.7634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10780  Z= 0.164
  Angle     :  0.736  12.517  14643  Z= 0.363
  Chirality :  0.043   0.274   1681
  Planarity :  0.005   0.050   1892
  Dihedral  :  6.306 130.684   1501
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 17.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.24), residues: 1329
  helix:  0.84 (0.20), residues: 705
  sheet: -1.60 (0.51), residues: 98
  loop : -1.76 (0.30), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  71 
 TYR   0.014   0.002   TYR A 286 
 PHE   0.031   0.002   PHE A 241 
 TRP   0.047   0.003   TRP A 308 
 HIS   0.009   0.001   HIS B 617 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (10776)
  covalent geometry    : angle       0.73557 (14643)
  hydrogen bonds       : bond        0.03583 (  499)
  hydrogen bonds       : angle       4.32702 ( 1452)
  metal coordination   : bond        0.00345 (    4)

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

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

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2658 Ramachandran restraints generated.
    1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 PHE cc_start: 0.7881 (m-80) cc_final: 0.7176 (m-80)
REVERT: A  201 LEU cc_start: 0.9264 (mt) cc_final: 0.8605 (mt)
REVERT: A  202 GLU cc_start: 0.8477 (tp30) cc_final: 0.7910 (tm-30)
REVERT: A  203 LEU cc_start: 0.8760 (tp) cc_final: 0.8391 (tp)
REVERT: A  210 MET cc_start: 0.9340 (mtm) cc_final: 0.8547 (ttm)
REVERT: A  280 ARG cc_start: 0.7139 (mmm-85) cc_final: 0.6218 (mmm-85)
REVERT: A  299 GLU cc_start: 0.9088 (tp30) cc_final: 0.8782 (tp30)
REVERT: A  324 PHE cc_start: 0.7278 (t80) cc_final: 0.7007 (t80)
REVERT: A  352 LEU cc_start: 0.9253 (mt) cc_final: 0.9032 (mt)
REVERT: A  370 MET cc_start: 0.7208 (mmp) cc_final: 0.6924 (mmm)
REVERT: A  600 MET cc_start: 0.8473 (mmp) cc_final: 0.7788 (tpt)
REVERT: A  657 MET cc_start: 0.7993 (mpp) cc_final: 0.7689 (mpp)
REVERT: B  155 TYR cc_start: 0.8349 (t80) cc_final: 0.7909 (t80)
REVERT: B  326 MET cc_start: 0.7466 (tpt) cc_final: 0.7125 (tpt)
REVERT: B  419 ASP cc_start: 0.7773 (p0) cc_final: 0.7387 (p0)
REVERT: B  523 ARG cc_start: 0.9257 (ppt170) cc_final: 0.8925 (ttt-90)
REVERT: B  535 HIS cc_start: 0.6368 (t70) cc_final: 0.6086 (t-90)
REVERT: B  695 LEU cc_start: 0.9486 (mm) cc_final: 0.9234 (mm)
REVERT: B  704 GLU cc_start: 0.9447 (pm20) cc_final: 0.8991 (pm20)
REVERT: B  737 LEU cc_start: 0.7493 (mt) cc_final: 0.7099 (mt)
REVERT: B  764 ILE cc_start: 0.9204 (mm) cc_final: 0.8966 (mm)
REVERT: C   45 VAL cc_start: 0.6705 (t) cc_final: 0.5995 (t)
REVERT: C   50 MET cc_start: 0.8028 (mtt) cc_final: 0.6748 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1109
  time to fit residues: 18.8114
Evaluate side-chains
  99 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 95 optimal weight:    7.9990
   chunk 78 optimal weight:    5.9990
   chunk 71 optimal weight:   20.0000
   chunk 72 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0170
   chunk 28 optimal weight:    8.9990
   chunk 15 optimal weight:    8.9990
   chunk 22 optimal weight:   20.0000
   chunk 47 optimal weight:   30.0000
   chunk 97 optimal weight:    9.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    4.2026

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 GLN
** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  67 ASN
C 119 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.076685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.063451 restraints weight = 62625.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.064856 restraints weight = 44679.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.065923 restraints weight = 34267.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.066655 restraints weight = 27609.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.067269 restraints weight = 23402.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.7835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10780  Z= 0.173
  Angle     :  0.731  12.262  14643  Z= 0.364
  Chirality :  0.043   0.264   1681
  Planarity :  0.005   0.050   1892
  Dihedral  :  6.306 129.697   1501
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 17.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.50 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.55 (0.24), residues: 1329
  helix:  0.84 (0.20), residues: 702
  sheet: -1.54 (0.52), residues: 96
  loop : -1.80 (0.30), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 261 
 TYR   0.014   0.002   TYR A 286 
 PHE   0.036   0.002   PHE A 241 
 TRP   0.046   0.003   TRP A 308 
 HIS   0.012   0.001   HIS B 617 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (10776)
  covalent geometry    : angle       0.73050 (14643)
  hydrogen bonds       : bond        0.03548 (  499)
  hydrogen bonds       : angle       4.41995 ( 1452)
  metal coordination   : bond        0.00352 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1655.91 seconds
wall clock time: 29 minutes 34.75 seconds (1774.75 seconds total)