Starting phenix.real_space_refine
on Thu Feb 13 10:40:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pw9_20501/02_2025/6pw9_20501.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pw9_20501/02_2025/6pw9_20501.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6pw9_20501/02_2025/6pw9_20501.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pw9_20501/02_2025/6pw9_20501.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pw9_20501/02_2025/6pw9_20501.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pw9_20501/02_2025/6pw9_20501.cif"
  }
  resolution = 4.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     S      56      5.16       5
     C    5597      2.51       5
     N    1508      2.21       5
     O    1666      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8836
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1260
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 1260
          Classifications: {'peptide': 155}
          Link IDs: {'PTRANS': 4, 'TRANS': 150}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
    Chain: "B"
      Number of atoms: 5470
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 665, 5470
          Classifications: {'peptide': 665}
          Link IDs: {'PTRANS': 27, 'TRANS': 637}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1287
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1287
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 160, 'undetermined': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'ACE_C-N': 1, 'PTRANS': 6, 'TRANS': 153}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 23
    Chain: "D"
      Number of atoms: 732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 732
          Classifications: {'peptide': 95}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'TRANS': 94}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "C"
      Number of atoms: 87
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 87
          Unusual residues: {'ACO': 1, 'IHP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.33, per 1000 atoms: 0.60
  Number of scatterers: 8836
  At special positions: 0
  Unit cell: (114.562, 100.534, 106.379, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      56     16.00
     P       9     15.00
     O    1666      8.00
     N    1508      7.00
     C    5597      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.23
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2078

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 3 sheets defined
      67.4% alpha, 8.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 26
      removed outlier: 4.107A  pdb=" N   LEU A  19 " --> pdb=" O   ASN A  15 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   VAL A  25 " --> pdb=" O   ARG A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 39
      removed outlier: 4.257A  pdb=" N   TYR A  36 " --> pdb=" O   ASN A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 45
      removed outlier: 3.726A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 42 through 45'
    Processing helix  chain 'A' and resid 88 through 104
      removed outlier: 3.924A  pdb=" N   MET A  92 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 126
    Processing helix  chain 'B' and resid 114 through 127
    Processing helix  chain 'B' and resid 129 through 144
      removed outlier: 3.528A  pdb=" N   TYR B 133 " --> pdb=" O   ASP B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 161
      removed outlier: 4.344A  pdb=" N   TRP B 151 " --> pdb=" O   GLN B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 176
      removed outlier: 4.139A  pdb=" N   LYS B 169 " --> pdb=" O   GLU B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 181
      removed outlier: 4.165A  pdb=" N   THR B 180 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   SER B 181 " --> pdb=" O   GLN B 178 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 177 through 181'
    Processing helix  chain 'B' and resid 185 through 203
      removed outlier: 4.488A  pdb=" N   TYR B 189 " --> pdb=" O   VAL B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 216
    Processing helix  chain 'B' and resid 217 through 220
      removed outlier: 4.008A  pdb=" N   ILE B 220 " --> pdb=" O   GLU B 217 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 217 through 220'
    Processing helix  chain 'B' and resid 222 through 237
      removed outlier: 4.155A  pdb=" N   VAL B 226 " --> pdb=" O   ASP B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 240 through 254
    Processing helix  chain 'B' and resid 257 through 269
      removed outlier: 3.880A  pdb=" N   TYR B 261 " --> pdb=" O   ASN B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 287
      removed outlier: 3.824A  pdb=" N   ILE B 279 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   TYR B 280 " --> pdb=" O   ARG B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 295
    Processing helix  chain 'B' and resid 296 through 301
      removed outlier: 4.432A  pdb=" N   PHE B 300 " --> pdb=" O   LEU B 296 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU B 301 " --> pdb=" O   PRO B 297 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 296 through 301'
    Processing helix  chain 'B' and resid 303 through 320
      removed outlier: 3.627A  pdb=" N   LYS B 312 " --> pdb=" O   GLU B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 330
    Processing helix  chain 'B' and resid 336 through 357
      removed outlier: 4.479A  pdb=" N   SER B 355 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 388
      removed outlier: 4.242A  pdb=" N   LEU B 374 " --> pdb=" O   PRO B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 404
      removed outlier: 3.715A  pdb=" N   ALA B 393 " --> pdb=" O   GLN B 389 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   THR B 399 " --> pdb=" O   GLU B 395 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   THR B 404 " --> pdb=" O   ALA B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 420
      removed outlier: 4.049A  pdb=" N   PHE B 411 " --> pdb=" O   LEU B 407 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   TYR B 418 " --> pdb=" O   LYS B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 424 through 437
      removed outlier: 3.806A  pdb=" N   GLU B 433 " --> pdb=" O   ARG B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 454
      removed outlier: 4.201A  pdb=" N   ASN B 445 " --> pdb=" O   ASP B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 466
    Processing helix  chain 'B' and resid 474 through 482
    Processing helix  chain 'B' and resid 484 through 498
      removed outlier: 3.739A  pdb=" N   GLN B 488 " --> pdb=" O   CYS B 484 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 501 through 521
    Processing helix  chain 'B' and resid 522 through 524
      No H-bonds generated for 'chain 'B' and resid 522 through 524'
    Processing helix  chain 'B' and resid 525 through 532
    Processing helix  chain 'B' and resid 535 through 547
      removed outlier: 3.570A  pdb=" N   VAL B 547 " --> pdb=" O   LYS B 543 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 548 through 550
      No H-bonds generated for 'chain 'B' and resid 548 through 550'
    Processing helix  chain 'B' and resid 551 through 571
      removed outlier: 3.529A  pdb=" N   PHE B 555 " --> pdb=" O   HIS B 551 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   ILE B 560 " --> pdb=" O   LYS B 556 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 643 through 648
    Processing helix  chain 'B' and resid 653 through 668
      Proline residue:  B 663  - end of helix
      removed outlier: 3.579A  pdb=" N   VAL B 668 " --> pdb=" O   LEU B 664 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 671 through 683
      removed outlier: 4.281A  pdb=" N   HIS B 675 " --> pdb=" O   LYS B 671 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 700
    Processing helix  chain 'B' and resid 705 through 722
    Processing helix  chain 'B' and resid 727 through 742
      removed outlier: 3.732A  pdb=" N   THR B 732 " --> pdb=" O   ASP B 728 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   VAL B 733 " --> pdb=" O   THR B 729 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 746 through 758
      removed outlier: 3.530A  pdb=" N   PHE B 750 " --> pdb=" O   ASN B 746 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 761 through 775
      removed outlier: 3.797A  pdb=" N   MET B 771 " --> pdb=" O   SER B 767 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   TYR B 773 " --> pdb=" O   ALA B 769 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 776 through 778
      No H-bonds generated for 'chain 'B' and resid 776 through 778'
    Processing helix  chain 'B' and resid 779 through 787
    Processing helix  chain 'B' and resid 798 through 811
    Processing helix  chain 'B' and resid 820 through 832
      removed outlier: 3.824A  pdb=" N   LYS B 830 " --> pdb=" O   ALA B 826 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU B 831 " --> pdb=" O   ASN B 827 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 835 through 839
      removed outlier: 3.674A  pdb=" N   PHE B 838 " --> pdb=" O   ALA B 835 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   MET B 839 " --> pdb=" O   LEU B 836 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 835 through 839'
    Processing helix  chain 'C' and resid 7 through 12
      removed outlier: 3.588A  pdb=" N   LEU C  11 " --> pdb=" O   ARG C   7 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   MET C  12 " --> pdb=" O   PRO C   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 7 through 12'
    Processing helix  chain 'C' and resid 13 through 22
      removed outlier: 3.548A  pdb=" N   CYS C  17 " --> pdb=" O   ASN C  13 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 35
      removed outlier: 3.739A  pdb=" N   TYR C  31 " --> pdb=" O   GLN C  27 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 82
      removed outlier: 3.605A  pdb=" N   ARG C  82 " --> pdb=" O   ARG C  79 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 79 through 82'
    Processing helix  chain 'C' and resid 86 through 102
    Processing helix  chain 'C' and resid 116 through 124
    Processing helix  chain 'C' and resid 151 through 159
    Processing helix  chain 'D' and resid 60 through 85
      removed outlier: 3.961A  pdb=" N   VAL D  66 " --> pdb=" O   THR D  62 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLU D  82 " --> pdb=" O   LYS D  78 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 91 through 103
      removed outlier: 3.845A  pdb=" N   LEU D  95 " --> pdb=" O   LYS D  91 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   GLU D 103 " --> pdb=" O   MET D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 115
      removed outlier: 3.528A  pdb=" N   ALA D 109 " --> pdb=" O   SER D 105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 129
    Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 10
      removed outlier: 6.222A  pdb=" N   PHE A  51 " --> pdb=" O   ALA A  55 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   ALA A  55 " --> pdb=" O   PHE A  51 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   ALA A  58 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   LEU A  77 " --> pdb=" O   ALA A  58 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   CYS A  60 " --> pdb=" O   MET A  75 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   SER A  66 " --> pdb=" O   GLN A  69 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLN A  69 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   ASN A 108 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ILE A  74 " --> pdb=" O   TYR A 110 " (cutoff:3.500A)
      removed outlier: 5.875A  pdb=" N   HIS A 112 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
      removed outlier: 8.190A  pdb=" N   THR A  76 " --> pdb=" O   HIS A 112 " (cutoff:3.500A)
      removed outlier: 13.145A  pdb=" N   GLN A 114 " --> pdb=" O   THR A  76 " (cutoff:3.500A)
      removed outlier: 14.820A  pdb=" N   GLY A  78 " --> pdb=" O   GLN A 114 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   GLU A 133 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   GLN A 151 " --> pdb=" O   ILE A 131 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   ILE A 131 " --> pdb=" O   GLN A 151 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 2 through 5
      removed outlier: 8.378A  pdb=" N   VAL C  53 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   VAL C  77 " --> pdb=" O   VAL C  53 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   TYR C  55 " --> pdb=" O   LEU C  75 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   LEU C  75 " --> pdb=" O   TYR C  55 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   LEU C  57 " --> pdb=" O   THR C  73 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   HIS C  69 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 106 through 112
      removed outlier: 3.685A  pdb=" N   GLU C 132 " --> pdb=" O   ALA C 146 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   LYS C 148 " --> pdb=" O   ILE C 130 " (cutoff:3.500A)
      removed outlier: 5.359A  pdb=" N   ILE C 130 " --> pdb=" O   LYS C 148 " (cutoff:3.500A)

    483 hydrogen bonds defined for protein.
    1428 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.56

  Time building geometry restraints manager: 2.60 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: 1481
        1.30 -     1.43: 2253
        1.43 -     1.56: 5168
        1.56 -     1.69: 15
        1.69 -     1.82: 91
  Bond restraints: 9008
  Sorted by residual:
  bond pdb=" C1B ACO C 902 "
       pdb=" O4B ACO C 902 "
    ideal  model  delta    sigma   weight residual
    1.416  1.660 -0.244 1.40e-02 5.10e+03 3.05e+02
  bond pdb=" C1B ACO C 902 "
       pdb=" C2B ACO C 902 "
    ideal  model  delta    sigma   weight residual
    1.531  1.345  0.186 1.20e-02 6.94e+03 2.39e+02
  bond pdb=" C5P ACO C 902 "
       pdb=" N4P ACO C 902 "
    ideal  model  delta    sigma   weight residual
    1.331  1.498 -0.167 1.20e-02 6.94e+03 1.93e+02
  bond pdb=" C6A ACO C 902 "
       pdb=" N6A ACO C 902 "
    ideal  model  delta    sigma   weight residual
    1.337  1.463 -0.126 1.00e-02 1.00e+04 1.58e+02
  bond pdb=" O3A ACO C 902 "
       pdb=" P2A ACO C 902 "
    ideal  model  delta    sigma   weight residual
    1.592  1.723 -0.131 1.10e-02 8.26e+03 1.43e+02
  ... (remaining 9003 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.03: 11811
        3.03 -     6.06: 264
        6.06 -     9.09: 63
        9.09 -    12.13: 19
       12.13 -    15.16: 3
  Bond angle restraints: 12160
  Sorted by residual:
  angle pdb=" P1A ACO C 902 "
        pdb=" O3A ACO C 902 "
        pdb=" P2A ACO C 902 "
      ideal   model   delta    sigma   weight residual
     136.83  121.67   15.16 1.00e+00 1.00e+00 2.30e+02
  angle pdb=" N1A ACO C 902 "
        pdb=" C6A ACO C 902 "
        pdb=" N6A ACO C 902 "
      ideal   model   delta    sigma   weight residual
     118.11  104.50   13.61 1.23e+00 6.64e-01 1.23e+02
  angle pdb=" C5A ACO C 902 "
        pdb=" C6A ACO C 902 "
        pdb=" N6A ACO C 902 "
      ideal   model   delta    sigma   weight residual
     123.59  134.97  -11.38 1.08e+00 8.64e-01 1.12e+02
  angle pdb=" N1A ACO C 902 "
        pdb=" C2A ACO C 902 "
        pdb=" N3A ACO C 902 "
      ideal   model   delta    sigma   weight residual
     128.69  119.33    9.36 1.00e+00 1.00e+00 8.76e+01
  angle pdb=" C5A ACO C 902 "
        pdb=" C4A ACO C 902 "
        pdb=" N3A ACO C 902 "
      ideal   model   delta    sigma   weight residual
     126.80  118.30    8.50 1.00e+00 1.00e+00 7.22e+01
  ... (remaining 12155 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.35: 5284
       26.35 -    52.71: 272
       52.71 -    79.06: 21
       79.06 -   105.41: 3
      105.41 -   131.77: 7
  Dihedral angle restraints: 5587
    sinusoidal: 2384
      harmonic: 3203
  Sorted by residual:
  dihedral pdb=" CA  LYS B 500 "
           pdb=" C   LYS B 500 "
           pdb=" N   PHE B 501 "
           pdb=" CA  PHE B 501 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.02  -29.98     0      5.00e+00 4.00e-02 3.60e+01
  dihedral pdb=" CA  VAL B 185 "
           pdb=" C   VAL B 185 "
           pdb=" N   ASP B 186 "
           pdb=" CA  ASP B 186 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.95  -27.05     0      5.00e+00 4.00e-02 2.93e+01
  dihedral pdb=" CA  PHE C 102 "
           pdb=" C   PHE C 102 "
           pdb=" N   ASN C 103 "
           pdb=" CA  ASN C 103 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.32   25.68     0      5.00e+00 4.00e-02 2.64e+01
  ... (remaining 5584 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.011: 1324
       1.011 -    2.022: 0
       2.022 -    3.034: 0
       3.034 -    4.045: 0
       4.045 -    5.056: 3
  Chirality restraints: 1327
  Sorted by residual:
  chirality pdb=" C4  IHP C 901 "
            pdb=" C3  IHP C 901 "
            pdb=" C5  IHP C 901 "
            pdb=" O14 IHP C 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48   -2.58    5.06 2.00e-01 2.50e+01 6.39e+02
  chirality pdb=" C2  IHP C 901 "
            pdb=" C1  IHP C 901 "
            pdb=" C3  IHP C 901 "
            pdb=" O12 IHP C 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52    2.50   -5.02 2.00e-01 2.50e+01 6.30e+02
  chirality pdb=" C1  IHP C 901 "
            pdb=" C2  IHP C 901 "
            pdb=" C6  IHP C 901 "
            pdb=" O11 IHP C 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.32   -2.48    4.80 2.00e-01 2.50e+01 5.75e+02
  ... (remaining 1324 not shown)

  Planarity restraints: 1549
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 143 "   -0.100 5.00e-02 4.00e+02   1.49e-01 3.56e+01
        pdb=" N   PRO A 144 "    0.258 5.00e-02 4.00e+02
        pdb=" CA  PRO A 144 "   -0.086 5.00e-02 4.00e+02
        pdb=" CD  PRO A 144 "   -0.072 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 707 "   -0.020 2.00e-02 2.50e+03   1.73e-02 7.45e+00
        pdb=" CG  TRP B 707 "    0.047 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 707 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 707 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 707 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 707 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 707 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 707 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 707 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 707 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 565 "    0.015 2.00e-02 2.50e+03   1.74e-02 6.08e+00
        pdb=" CG  TYR B 565 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 565 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 565 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 565 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 565 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 565 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 565 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1546 not shown)

  Histogram of nonbonded interaction distances:
        1.78 -     2.40: 15
        2.40 -     3.03: 4155
        3.03 -     3.65: 13924
        3.65 -     4.28: 18970
        4.28 -     4.90: 30417
  Nonbonded interactions: 67481
  Sorted by model distance:
  nonbonded pdb=" O   PRO A  13 "
            pdb=" CD1 ILE A  16 "
     model   vdw
     1.781 3.460
  nonbonded pdb=" OE2 GLU B 191 "
            pdb=" O   ILE B 533 "
     model   vdw
     1.914 3.040
  nonbonded pdb=" O   GLU A 143 "
            pdb=" OE1 GLU A 143 "
     model   vdw
     1.918 3.040
  nonbonded pdb=" CE2 TYR B 528 "
            pdb=" CE  LYS B 532 "
     model   vdw
     2.180 3.740
  nonbonded pdb=" O   ILE B 784 "
            pdb=" OG1 THR B 788 "
     model   vdw
     2.260 3.040
  ... (remaining 67476 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:             0.450
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.340
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6994
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      :  0.007   0.244   9008  Z= 0.496
  Angle     :  1.226  15.157  12160  Z= 0.667
  Chirality :  0.244   5.056   1327
  Planarity :  0.008   0.149   1549
  Dihedral  : 15.091 131.767   3509
  Min Nonbonded Distance : 1.781

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  8.18 %
    Favored  : 90.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.47 (0.20), residues: 1065
  helix: -2.86 (0.15), residues: 637
  sheet: -2.24 (0.57), residues: 71
  loop : -2.92 (0.27), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.003   TRP B 707 
 HIS   0.007   0.002   HIS A 148 
 PHE   0.030   0.003   PHE B 716 
 TYR   0.042   0.003   TYR B 565 
 ARG   0.007   0.001   ARG B 714 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 302
  time to evaluate  : 0.900 
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: A   94 ASN cc_start: 0.7985 (m-40) cc_final: 0.7342 (t0)
REVERT: A   99 ILE cc_start: 0.8686 (pp) cc_final: 0.8269 (pp)
REVERT: B  450 LYS cc_start: 0.7847 (ttpt) cc_final: 0.7600 (ttmm)
REVERT: B  459 LYS cc_start: 0.8611 (ptpp) cc_final: 0.7916 (tppt)
REVERT: B  503 GLU cc_start: 0.5474 (pp20) cc_final: 0.4958 (pt0)
REVERT: B  528 TYR cc_start: 0.6315 (t80) cc_final: 0.5999 (t80)
REVERT: B  775 LEU cc_start: 0.8055 (mm) cc_final: 0.7676 (mm)
REVERT: B  803 MET cc_start: 0.8045 (tmm) cc_final: 0.7723 (tmm)
REVERT: C   25 ASN cc_start: 0.8128 (m-40) cc_final: 0.7792 (m-40)
REVERT: D   60 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8155 (tm)
REVERT: D   92 LYS cc_start: 0.8644 (mppt) cc_final: 0.7998 (tptt)
  outliers start: 17
  outliers final: 5
  residues processed: 316
  average time/residue: 0.2680
  time to fit residues: 110.7373
Evaluate side-chains
  192 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 186
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 80 optimal weight:    7.9990
   chunk 44 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 50 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 96 optimal weight:    9.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
A  65 HIS
A 114 GLN
A 148 HIS
** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 196 GLN
B 197 ASN
B 212 HIS
** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 569 HIS
C  71 HIS
C 120 HIS
D  36 HIS
D 116 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.147274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.120445 restraints weight = 19801.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.123383 restraints weight = 12115.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.125380 restraints weight = 8639.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9008  Z= 0.209
  Angle     :  0.756   9.720  12160  Z= 0.379
  Chirality :  0.047   0.301   1327
  Planarity :  0.005   0.066   1549
  Dihedral  : 10.218  62.007   1281
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  5.95 %
    Favored  : 93.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.72 (0.23), residues: 1065
  helix: -1.37 (0.19), residues: 647
  sheet: -1.96 (0.65), residues: 62
  loop : -2.32 (0.29), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 707 
 HIS   0.006   0.001   HIS A  95 
 PHE   0.019   0.002   PHE B 716 
 TYR   0.017   0.002   TYR A  73 
 ARG   0.005   0.000   ARG B 118 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 250
  time to evaluate  : 1.010 
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   53 ASP cc_start: 0.6991 (m-30) cc_final: 0.6694 (t70)
REVERT: A   94 ASN cc_start: 0.8000 (m-40) cc_final: 0.7313 (t0)
REVERT: A   98 ASN cc_start: 0.8589 (p0) cc_final: 0.8362 (p0)
REVERT: A  138 TYR cc_start: 0.7878 (t80) cc_final: 0.7274 (t80)
REVERT: A  141 ARG cc_start: 0.7989 (mpp80) cc_final: 0.7712 (mpp80)
REVERT: A  146 ASP cc_start: 0.7263 (m-30) cc_final: 0.6438 (t70)
REVERT: A  148 HIS cc_start: 0.7549 (m90) cc_final: 0.7251 (m-70)
REVERT: B  166 MET cc_start: 0.3922 (ppp) cc_final: 0.3483 (ppp)
REVERT: B  191 GLU cc_start: 0.7779 (pp20) cc_final: 0.7443 (tp30)
REVERT: B  278 LYS cc_start: 0.8193 (mttt) cc_final: 0.7665 (mmtm)
REVERT: B  358 LEU cc_start: 0.7087 (tp) cc_final: 0.6828 (pt)
REVERT: B  366 LYS cc_start: 0.7381 (pptt) cc_final: 0.6837 (tmtt)
REVERT: B  447 LYS cc_start: 0.8083 (mttt) cc_final: 0.7818 (mttt)
REVERT: B  490 GLU cc_start: 0.8469 (tp30) cc_final: 0.8233 (tp30)
REVERT: B  551 HIS cc_start: 0.8097 (t-90) cc_final: 0.7405 (t70)
REVERT: B  672 ILE cc_start: 0.7254 (pt) cc_final: 0.7044 (pt)
REVERT: B  726 LEU cc_start: 0.7593 (pp) cc_final: 0.6586 (tp)
REVERT: B  734 LEU cc_start: 0.9030 (tt) cc_final: 0.8613 (pp)
REVERT: B  749 ASN cc_start: 0.8699 (m110) cc_final: 0.8438 (p0)
REVERT: B  803 MET cc_start: 0.8202 (tmm) cc_final: 0.7678 (tmm)
REVERT: C   12 MET cc_start: 0.8196 (tmm) cc_final: 0.7889 (tmm)
REVERT: C   98 MET cc_start: 0.8295 (mtp) cc_final: 0.8004 (mtm)
REVERT: C  101 ASN cc_start: 0.8765 (p0) cc_final: 0.8525 (p0)
REVERT: D   91 LYS cc_start: 0.8707 (tttp) cc_final: 0.8325 (mtmt)
REVERT: D   92 LYS cc_start: 0.8497 (mppt) cc_final: 0.7758 (tptt)
REVERT: D  106 ARG cc_start: 0.6893 (tmm-80) cc_final: 0.6667 (ttp80)
  outliers start: 7
  outliers final: 1
  residues processed: 256
  average time/residue: 0.2329
  time to fit residues: 79.2500
Evaluate side-chains
  186 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 185
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 35 optimal weight:    0.0770
   chunk 63 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 22 optimal weight:    0.2980
   chunk 84 optimal weight:    0.5980
   chunk 69 optimal weight:   10.0000
   chunk 42 optimal weight:    1.9990
   chunk 15 optimal weight:    7.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    1.1942

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

Flipped N/Q/H residues before XYZ refinement:
** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 478 ASN
B 509 HIS
B 736 GLN
D 116 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.146262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.119172 restraints weight = 20229.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.122041 restraints weight = 12313.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.123933 restraints weight = 8813.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9008  Z= 0.195
  Angle     :  0.709   8.988  12160  Z= 0.358
  Chirality :  0.046   0.233   1327
  Planarity :  0.004   0.042   1549
  Dihedral  :  9.479  59.809   1281
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  5.53 %
    Favored  : 93.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (0.24), residues: 1065
  helix: -0.89 (0.19), residues: 649
  sheet: -1.80 (0.68), residues: 57
  loop : -2.15 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 707 
 HIS   0.006   0.001   HIS A  95 
 PHE   0.024   0.002   PHE B 515 
 TYR   0.020   0.002   TYR B 154 
 ARG   0.004   0.000   ARG B 429 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 241
  time to evaluate  : 0.846 
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   53 ASP cc_start: 0.7079 (m-30) cc_final: 0.6819 (t70)
REVERT: A   94 ASN cc_start: 0.8205 (m-40) cc_final: 0.7307 (t0)
REVERT: A   98 ASN cc_start: 0.8581 (p0) cc_final: 0.8378 (p0)
REVERT: A  138 TYR cc_start: 0.7861 (t80) cc_final: 0.7552 (t80)
REVERT: A  141 ARG cc_start: 0.8025 (mpp80) cc_final: 0.7743 (mpp80)
REVERT: A  146 ASP cc_start: 0.7239 (m-30) cc_final: 0.6863 (m-30)
REVERT: A  148 HIS cc_start: 0.7392 (m90) cc_final: 0.7019 (m-70)
REVERT: B  158 TYR cc_start: 0.7613 (m-80) cc_final: 0.6868 (m-80)
REVERT: B  166 MET cc_start: 0.3384 (ppp) cc_final: 0.2684 (ppp)
REVERT: B  191 GLU cc_start: 0.7927 (pp20) cc_final: 0.7462 (tp30)
REVERT: B  291 LEU cc_start: 0.8463 (tp) cc_final: 0.8254 (tp)
REVERT: B  366 LYS cc_start: 0.7515 (pptt) cc_final: 0.6952 (tmtt)
REVERT: B  495 TYR cc_start: 0.5419 (t80) cc_final: 0.4861 (t80)
REVERT: B  505 LEU cc_start: 0.8622 (tt) cc_final: 0.8412 (mp)
REVERT: B  551 HIS cc_start: 0.8110 (t-90) cc_final: 0.7511 (t-90)
REVERT: B  734 LEU cc_start: 0.9115 (tt) cc_final: 0.8797 (tt)
REVERT: B  749 ASN cc_start: 0.8668 (m110) cc_final: 0.8336 (p0)
REVERT: B  771 MET cc_start: 0.8546 (mmm) cc_final: 0.8247 (mmm)
REVERT: B  803 MET cc_start: 0.8255 (tmm) cc_final: 0.7697 (tmm)
REVERT: C   12 MET cc_start: 0.8294 (tmm) cc_final: 0.7902 (tmm)
REVERT: D   91 LYS cc_start: 0.8749 (tttp) cc_final: 0.8322 (mtmt)
REVERT: D   92 LYS cc_start: 0.8614 (mppt) cc_final: 0.7848 (tptt)
REVERT: D  106 ARG cc_start: 0.6923 (tmm-80) cc_final: 0.6643 (ttp80)
REVERT: D  115 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7345 (mp0)
  outliers start: 5
  outliers final: 1
  residues processed: 243
  average time/residue: 0.2198
  time to fit residues: 72.7520
Evaluate side-chains
  187 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 186
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 87 optimal weight:   20.0000
   chunk 68 optimal weight:    0.8980
   chunk 51 optimal weight:    7.9990
   chunk 23 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 55 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0870
   overall best weight:    1.1962

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

Flipped N/Q/H residues before XYZ refinement:
** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 478 ASN
C  71 HIS
D 116 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.145257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.117987 restraints weight = 20026.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.120790 restraints weight = 12201.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.122637 restraints weight = 8752.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7234
moved from start:          0.3872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9008  Z= 0.203
  Angle     :  0.704   8.722  12160  Z= 0.355
  Chirality :  0.046   0.214   1327
  Planarity :  0.004   0.037   1549
  Dihedral  :  9.095  57.558   1281
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  4.68 %
    Favored  : 95.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.24), residues: 1065
  helix: -0.62 (0.19), residues: 650
  sheet: -1.73 (0.71), residues: 55
  loop : -1.96 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 707 
 HIS   0.008   0.001   HIS B 526 
 PHE   0.016   0.002   PHE B 716 
 TYR   0.020   0.002   TYR B 154 
 ARG   0.007   0.000   ARG B 134 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 238
  time to evaluate  : 0.807 
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   53 ASP cc_start: 0.7044 (m-30) cc_final: 0.6810 (t70)
REVERT: A   90 THR cc_start: 0.7458 (m) cc_final: 0.7006 (m)
REVERT: A   94 ASN cc_start: 0.8150 (m-40) cc_final: 0.7534 (m110)
REVERT: A  138 TYR cc_start: 0.7800 (t80) cc_final: 0.7589 (t80)
REVERT: A  141 ARG cc_start: 0.7920 (mpp80) cc_final: 0.7670 (mpp80)
REVERT: A  146 ASP cc_start: 0.7412 (m-30) cc_final: 0.6935 (m-30)
REVERT: B  166 MET cc_start: 0.3780 (ppp) cc_final: 0.2982 (ppp)
REVERT: B  366 LYS cc_start: 0.7502 (pptt) cc_final: 0.6922 (tmtt)
REVERT: B  430 TRP cc_start: 0.6933 (m100) cc_final: 0.6556 (m100)
REVERT: B  495 TYR cc_start: 0.5556 (t80) cc_final: 0.5036 (t80)
REVERT: B  551 HIS cc_start: 0.8236 (t-90) cc_final: 0.7612 (t-90)
REVERT: B  726 LEU cc_start: 0.7623 (pp) cc_final: 0.6711 (tp)
REVERT: B  734 LEU cc_start: 0.9199 (tt) cc_final: 0.8909 (tp)
REVERT: B  803 MET cc_start: 0.8287 (tmm) cc_final: 0.7694 (tmm)
REVERT: B  827 ASN cc_start: 0.8148 (t0) cc_final: 0.7854 (t0)
REVERT: C   12 MET cc_start: 0.8201 (tmm) cc_final: 0.7770 (tmm)
REVERT: D   91 LYS cc_start: 0.8702 (tttp) cc_final: 0.8295 (mtmt)
REVERT: D   92 LYS cc_start: 0.8627 (mppt) cc_final: 0.7869 (tptt)
REVERT: D  115 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7361 (mp0)
  outliers start: 3
  outliers final: 0
  residues processed: 241
  average time/residue: 0.2115
  time to fit residues: 70.2947
Evaluate side-chains
  197 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 84 optimal weight:    3.9990
   chunk 102 optimal weight:    9.9990
   chunk 97 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 22 optimal weight:    9.9990
   chunk 36 optimal weight:    0.7980
   chunk 40 optimal weight:    9.9990
   chunk 13 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 478 ASN
B 736 GLN
C   5 ASN
D 116 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.142420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.115090 restraints weight = 20245.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.117792 restraints weight = 12710.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.119640 restraints weight = 9241.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.4272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9008  Z= 0.225
  Angle     :  0.733  10.330  12160  Z= 0.371
  Chirality :  0.047   0.231   1327
  Planarity :  0.004   0.053   1549
  Dihedral  :  8.964  56.175   1281
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.25), residues: 1065
  helix: -0.53 (0.20), residues: 659
  sheet: -1.79 (0.70), residues: 55
  loop : -1.87 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C  38 
 HIS   0.009   0.001   HIS B 514 
 PHE   0.030   0.002   PHE B 515 
 TYR   0.014   0.002   TYR B 154 
 ARG   0.011   0.001   ARG B 134 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 1.018 
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: A    7 GLU cc_start: 0.8234 (tp30) cc_final: 0.8027 (mm-30)
REVERT: A   53 ASP cc_start: 0.7043 (m-30) cc_final: 0.6823 (t70)
REVERT: A   94 ASN cc_start: 0.8116 (m-40) cc_final: 0.7186 (t0)
REVERT: A   98 ASN cc_start: 0.8642 (p0) cc_final: 0.8420 (p0)
REVERT: A  141 ARG cc_start: 0.7990 (mpp80) cc_final: 0.7675 (mpp80)
REVERT: A  146 ASP cc_start: 0.7445 (m-30) cc_final: 0.6938 (m-30)
REVERT: B  166 MET cc_start: 0.3979 (ppp) cc_final: 0.3540 (ppp)
REVERT: B  291 LEU cc_start: 0.8637 (tp) cc_final: 0.8336 (tp)
REVERT: B  366 LYS cc_start: 0.7646 (pptt) cc_final: 0.7041 (tmtt)
REVERT: B  430 TRP cc_start: 0.6987 (m100) cc_final: 0.6620 (m100)
REVERT: B  447 LYS cc_start: 0.8180 (mttt) cc_final: 0.7832 (ttmm)
REVERT: B  490 GLU cc_start: 0.8424 (tp30) cc_final: 0.8157 (tp30)
REVERT: B  551 HIS cc_start: 0.8357 (t-90) cc_final: 0.7926 (t-90)
REVERT: B  710 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7659 (mp0)
REVERT: B  803 MET cc_start: 0.8351 (tmm) cc_final: 0.7746 (tmm)
REVERT: B  827 ASN cc_start: 0.8100 (t0) cc_final: 0.7824 (t0)
REVERT: C  101 ASN cc_start: 0.8771 (p0) cc_final: 0.8544 (p0)
REVERT: C  137 TYR cc_start: 0.7411 (t80) cc_final: 0.7211 (t80)
REVERT: D   91 LYS cc_start: 0.8700 (tttp) cc_final: 0.8290 (mtmt)
REVERT: D   92 LYS cc_start: 0.8660 (mppt) cc_final: 0.7911 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.2116
  time to fit residues: 69.9423
Evaluate side-chains
  191 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 34 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 0 optimal weight:    9.9990
   chunk 61 optimal weight:    0.1980
   chunk 52 optimal weight:    5.9990
   chunk 2 optimal weight:    0.2980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 114 GLN
** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 478 ASN
B 736 GLN
C  71 HIS
D 116 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.142613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.115579 restraints weight = 19658.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.118417 restraints weight = 11788.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.120323 restraints weight = 8355.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.4552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9008  Z= 0.198
  Angle     :  0.718  11.468  12160  Z= 0.358
  Chirality :  0.046   0.224   1327
  Planarity :  0.004   0.061   1549
  Dihedral  :  8.745  55.569   1281
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.61 %
    Favored  : 96.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.25), residues: 1065
  helix: -0.34 (0.20), residues: 652
  sheet: -1.65 (0.67), residues: 59
  loop : -1.81 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 486 
 HIS   0.006   0.001   HIS B 526 
 PHE   0.019   0.002   PHE B 716 
 TYR   0.041   0.002   TYR B 154 
 ARG   0.004   0.000   ARG D 106 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 254
  time to evaluate  : 1.000 
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: A    7 GLU cc_start: 0.8407 (tp30) cc_final: 0.8163 (mm-30)
REVERT: A   90 THR cc_start: 0.7509 (m) cc_final: 0.7123 (m)
REVERT: A   94 ASN cc_start: 0.8271 (m-40) cc_final: 0.7669 (m110)
REVERT: A  141 ARG cc_start: 0.7982 (mpp80) cc_final: 0.7724 (mpp80)
REVERT: A  146 ASP cc_start: 0.7359 (m-30) cc_final: 0.6907 (m-30)
REVERT: B  166 MET cc_start: 0.3844 (ppp) cc_final: 0.3355 (ppp)
REVERT: B  291 LEU cc_start: 0.8530 (tp) cc_final: 0.8242 (tp)
REVERT: B  366 LYS cc_start: 0.7430 (pptt) cc_final: 0.6850 (tmtt)
REVERT: B  430 TRP cc_start: 0.7009 (m100) cc_final: 0.6675 (m100)
REVERT: B  447 LYS cc_start: 0.8093 (mttt) cc_final: 0.7795 (ttmm)
REVERT: B  450 LYS cc_start: 0.7941 (ttpt) cc_final: 0.7517 (ttmm)
REVERT: B  490 GLU cc_start: 0.8502 (tp30) cc_final: 0.8242 (tp30)
REVERT: B  523 PHE cc_start: 0.8557 (t80) cc_final: 0.8224 (t80)
REVERT: B  551 HIS cc_start: 0.8404 (t-90) cc_final: 0.7997 (t-90)
REVERT: B  710 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7693 (mp0)
REVERT: B  728 ASP cc_start: 0.7952 (p0) cc_final: 0.7204 (t0)
REVERT: B  734 LEU cc_start: 0.9290 (tt) cc_final: 0.9083 (tt)
REVERT: B  803 MET cc_start: 0.8304 (tmm) cc_final: 0.7696 (tmm)
REVERT: B  827 ASN cc_start: 0.8035 (t0) cc_final: 0.7732 (t0)
REVERT: C   46 GLU cc_start: 0.8112 (pt0) cc_final: 0.7865 (pt0)
REVERT: C  137 TYR cc_start: 0.7586 (t80) cc_final: 0.7334 (t80)
REVERT: D   91 LYS cc_start: 0.8699 (tttp) cc_final: 0.8274 (mtmt)
REVERT: D   92 LYS cc_start: 0.8702 (mppt) cc_final: 0.7952 (tptt)
  outliers start: 1
  outliers final: 1
  residues processed: 254
  average time/residue: 0.2277
  time to fit residues: 78.0164
Evaluate side-chains
  198 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 197
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 92 optimal weight:    9.9990
   chunk 32 optimal weight:    0.8980
   chunk 39 optimal weight:   10.0000
   chunk 47 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 10 optimal weight:    8.9990
   chunk 70 optimal weight:    6.9990
   chunk 61 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 7 optimal weight:    7.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 148 HIS
** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 478 ASN
D 116 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.141498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.114379 restraints weight = 20369.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.116981 restraints weight = 12885.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.118766 restraints weight = 9417.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.4813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9008  Z= 0.228
  Angle     :  0.749  11.569  12160  Z= 0.377
  Chirality :  0.048   0.222   1327
  Planarity :  0.004   0.038   1549
  Dihedral  :  8.781  58.530   1281
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  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 : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.25), residues: 1065
  helix: -0.31 (0.20), residues: 661
  sheet: -1.80 (0.59), residues: 68
  loop : -1.68 (0.32), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 486 
 HIS   0.007   0.001   HIS B 526 
 PHE   0.030   0.002   PHE B 515 
 TYR   0.028   0.002   TYR B 495 
 ARG   0.006   0.000   ARG B 134 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 254
  time to evaluate  : 0.965 
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    7 GLU cc_start: 0.8405 (tp30) cc_final: 0.8074 (mm-30)
REVERT: A   90 THR cc_start: 0.7498 (m) cc_final: 0.7244 (m)
REVERT: A  146 ASP cc_start: 0.7555 (m-30) cc_final: 0.7110 (m-30)
REVERT: B  166 MET cc_start: 0.4169 (ppp) cc_final: 0.3901 (ppp)
REVERT: B  291 LEU cc_start: 0.8443 (tp) cc_final: 0.8178 (tp)
REVERT: B  366 LYS cc_start: 0.7499 (pptt) cc_final: 0.6819 (tmtt)
REVERT: B  430 TRP cc_start: 0.7015 (m100) cc_final: 0.6773 (m100)
REVERT: B  447 LYS cc_start: 0.8228 (mttt) cc_final: 0.7950 (ttmm)
REVERT: B  450 LYS cc_start: 0.8045 (ttpt) cc_final: 0.7695 (ttmm)
REVERT: B  510 GLU cc_start: 0.7953 (pm20) cc_final: 0.7417 (pm20)
REVERT: B  551 HIS cc_start: 0.8374 (t-90) cc_final: 0.8043 (t-90)
REVERT: B  710 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7809 (mp0)
REVERT: B  728 ASP cc_start: 0.7644 (p0) cc_final: 0.6978 (t0)
REVERT: B  734 LEU cc_start: 0.9213 (tt) cc_final: 0.8938 (tt)
REVERT: B  803 MET cc_start: 0.8354 (tmm) cc_final: 0.7798 (tmm)
REVERT: B  827 ASN cc_start: 0.7880 (t0) cc_final: 0.7580 (t0)
REVERT: C  137 TYR cc_start: 0.7445 (t80) cc_final: 0.7192 (t80)
REVERT: D   91 LYS cc_start: 0.8661 (tttp) cc_final: 0.8251 (mtmt)
REVERT: D   92 LYS cc_start: 0.8714 (mppt) cc_final: 0.7982 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 254
  average time/residue: 0.2264
  time to fit residues: 78.0654
Evaluate side-chains
  195 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 81 optimal weight:    8.9990
   chunk 3 optimal weight:    8.9990
   chunk 88 optimal weight:    6.9990
   chunk 26 optimal weight:   20.0000
   chunk 65 optimal weight:    0.8980
   chunk 14 optimal weight:    5.9990
   chunk 56 optimal weight:    7.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 148 HIS
** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 124 GLN
B 383 HIS
B 478 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.138535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.113337 restraints weight = 20505.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.114262 restraints weight = 12770.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.115902 restraints weight = 9522.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.5205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   9008  Z= 0.255
  Angle     :  0.787   9.717  12160  Z= 0.397
  Chirality :  0.049   0.229   1327
  Planarity :  0.004   0.066   1549
  Dihedral  :  8.885  63.021   1281
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.25), residues: 1065
  helix: -0.35 (0.20), residues: 656
  sheet: -1.86 (0.56), residues: 65
  loop : -1.61 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 486 
 HIS   0.006   0.001   HIS B 526 
 PHE   0.023   0.002   PHE B 716 
 TYR   0.031   0.002   TYR B 495 
 ARG   0.006   0.001   ARG B 137 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 250
  time to evaluate  : 1.665 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8260 (mmm160) cc_final: 0.7994 (mmm160)
REVERT: A   94 ASN cc_start: 0.8052 (m110) cc_final: 0.7485 (m110)
REVERT: A  146 ASP cc_start: 0.7517 (m-30) cc_final: 0.7043 (m-30)
REVERT: B  166 MET cc_start: 0.4341 (ppp) cc_final: 0.4133 (ppp)
REVERT: B  291 LEU cc_start: 0.8629 (tp) cc_final: 0.8338 (tp)
REVERT: B  366 LYS cc_start: 0.7353 (pptt) cc_final: 0.6722 (tmtt)
REVERT: B  447 LYS cc_start: 0.8242 (mttt) cc_final: 0.7773 (ttmm)
REVERT: B  450 LYS cc_start: 0.8035 (ttpt) cc_final: 0.7479 (ttmm)
REVERT: B  452 MET cc_start: 0.6998 (mmp) cc_final: 0.6703 (mmp)
REVERT: B  453 LEU cc_start: 0.7373 (mt) cc_final: 0.7156 (mt)
REVERT: B  523 PHE cc_start: 0.8422 (t80) cc_final: 0.8116 (t80)
REVERT: B  551 HIS cc_start: 0.8564 (t-90) cc_final: 0.8176 (t-90)
REVERT: B  710 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7825 (mp0)
REVERT: B  734 LEU cc_start: 0.9356 (tt) cc_final: 0.8952 (tt)
REVERT: B  738 MET cc_start: 0.8948 (mpp) cc_final: 0.8530 (mpp)
REVERT: B  803 MET cc_start: 0.8356 (tmm) cc_final: 0.7740 (tmm)
REVERT: B  827 ASN cc_start: 0.8054 (t0) cc_final: 0.7757 (t0)
REVERT: C  137 TYR cc_start: 0.7945 (t80) cc_final: 0.7576 (t80)
REVERT: D   91 LYS cc_start: 0.8671 (tttp) cc_final: 0.8330 (mtmt)
REVERT: D   92 LYS cc_start: 0.8783 (mppt) cc_final: 0.8184 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 250
  average time/residue: 0.2363
  time to fit residues: 79.8152
Evaluate side-chains
  184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 70 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   chunk 45 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 80 optimal weight:    0.3980
   chunk 84 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 159 HIS
B 178 GLN
B 478 ASN
D 116 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.140969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.114282 restraints weight = 19877.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.117048 restraints weight = 12181.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.118986 restraints weight = 8717.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.5327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9008  Z= 0.205
  Angle     :  0.761  10.795  12160  Z= 0.379
  Chirality :  0.048   0.218   1327
  Planarity :  0.004   0.041   1549
  Dihedral  :  8.612  62.235   1281
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.06 %
    Favored  : 98.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.25), residues: 1065
  helix: -0.21 (0.20), residues: 653
  sheet: -1.82 (0.56), residues: 64
  loop : -1.58 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 486 
 HIS   0.007   0.001   HIS B 526 
 PHE   0.025   0.002   PHE B 515 
 TYR   0.031   0.002   TYR B 495 
 ARG   0.010   0.001   ARG A 141 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 250
  time to evaluate  : 1.146 
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   21 ARG cc_start: 0.8281 (mmm160) cc_final: 0.8028 (mmm160)
REVERT: A  146 ASP cc_start: 0.7543 (m-30) cc_final: 0.7037 (m-30)
REVERT: B  191 GLU cc_start: 0.8157 (pt0) cc_final: 0.7903 (pt0)
REVERT: B  291 LEU cc_start: 0.8533 (tp) cc_final: 0.8172 (tp)
REVERT: B  366 LYS cc_start: 0.7466 (pptt) cc_final: 0.6786 (tmtt)
REVERT: B  447 LYS cc_start: 0.8168 (mttt) cc_final: 0.7735 (ttmm)
REVERT: B  450 LYS cc_start: 0.8018 (ttpt) cc_final: 0.7420 (ttmm)
REVERT: B  523 PHE cc_start: 0.8335 (t80) cc_final: 0.8024 (t80)
REVERT: B  551 HIS cc_start: 0.8469 (t-90) cc_final: 0.8032 (t-170)
REVERT: B  710 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7849 (mp0)
REVERT: B  728 ASP cc_start: 0.7901 (p0) cc_final: 0.7157 (t0)
REVERT: B  734 LEU cc_start: 0.9299 (tt) cc_final: 0.8877 (tt)
REVERT: B  738 MET cc_start: 0.8801 (mpp) cc_final: 0.8465 (mpp)
REVERT: B  803 MET cc_start: 0.8306 (tmm) cc_final: 0.7719 (tmm)
REVERT: B  827 ASN cc_start: 0.8022 (t0) cc_final: 0.7744 (t0)
REVERT: C   59 LYS cc_start: 0.8855 (tttp) cc_final: 0.8376 (tttp)
REVERT: C   91 MET cc_start: 0.8118 (tpp) cc_final: 0.7848 (tpp)
REVERT: C  137 TYR cc_start: 0.7646 (t80) cc_final: 0.7314 (t80)
REVERT: D   91 LYS cc_start: 0.8760 (tttp) cc_final: 0.8320 (mtmt)
REVERT: D   92 LYS cc_start: 0.8960 (mppt) cc_final: 0.8095 (tptt)
  outliers start: 1
  outliers final: 0
  residues processed: 251
  average time/residue: 0.2118
  time to fit residues: 72.4065
Evaluate side-chains
  197 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0770
   chunk 60 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   chunk 51 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 80 optimal weight:    7.9990
   chunk 92 optimal weight:    5.9990
   chunk 105 optimal weight:    9.9990
   chunk 94 optimal weight:    0.1980
   overall best weight:    0.9742

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

Flipped N/Q/H residues before XYZ refinement:
A 148 HIS
** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 124 GLN
B 478 ASN
D 116 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.141026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.114323 restraints weight = 19992.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.117095 restraints weight = 12299.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.118951 restraints weight = 8814.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.5388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9008  Z= 0.200
  Angle     :  0.756  10.306  12160  Z= 0.376
  Chirality :  0.047   0.214   1327
  Planarity :  0.004   0.041   1549
  Dihedral  :  8.406  63.112   1281
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.25), residues: 1065
  helix: -0.15 (0.20), residues: 654
  sheet: -1.80 (0.56), residues: 64
  loop : -1.58 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 486 
 HIS   0.006   0.001   HIS B 526 
 PHE   0.020   0.002   PHE C 102 
 TYR   0.027   0.002   TYR B 154 
 ARG   0.009   0.001   ARG A 141 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 1.031 
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   21 ARG cc_start: 0.8257 (mmm160) cc_final: 0.8024 (mmm160)
REVERT: A  146 ASP cc_start: 0.7569 (m-30) cc_final: 0.7092 (m-30)
REVERT: B  173 GLU cc_start: 0.7884 (pp20) cc_final: 0.7612 (pp20)
REVERT: B  291 LEU cc_start: 0.8476 (tp) cc_final: 0.8148 (tp)
REVERT: B  366 LYS cc_start: 0.7457 (pptt) cc_final: 0.6780 (tmtt)
REVERT: B  447 LYS cc_start: 0.8103 (mttt) cc_final: 0.7753 (ttmm)
REVERT: B  450 LYS cc_start: 0.8077 (ttpt) cc_final: 0.7524 (ttmm)
REVERT: B  490 GLU cc_start: 0.8500 (tp30) cc_final: 0.8117 (tp30)
REVERT: B  551 HIS cc_start: 0.8438 (t-90) cc_final: 0.7956 (t70)
REVERT: B  710 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7846 (mp0)
REVERT: B  728 ASP cc_start: 0.7828 (p0) cc_final: 0.7059 (t0)
REVERT: B  734 LEU cc_start: 0.9283 (tt) cc_final: 0.8867 (tt)
REVERT: B  737 GLU cc_start: 0.7801 (mp0) cc_final: 0.7523 (mm-30)
REVERT: B  738 MET cc_start: 0.8826 (mpp) cc_final: 0.8549 (mpp)
REVERT: B  803 MET cc_start: 0.8295 (tmm) cc_final: 0.7709 (tmm)
REVERT: C   46 GLU cc_start: 0.8028 (pt0) cc_final: 0.7821 (pt0)
REVERT: C   59 LYS cc_start: 0.8739 (tttp) cc_final: 0.8275 (tttp)
REVERT: C  134 GLU cc_start: 0.7449 (tp30) cc_final: 0.7236 (mm-30)
REVERT: C  137 TYR cc_start: 0.7751 (t80) cc_final: 0.7393 (t80)
REVERT: D   91 LYS cc_start: 0.8602 (tttp) cc_final: 0.8243 (mtmt)
REVERT: D   92 LYS cc_start: 0.8792 (mppt) cc_final: 0.8129 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 245
  average time/residue: 0.2163
  time to fit residues: 73.1122
Evaluate side-chains
  190 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 82 optimal weight:    1.9990
   chunk 99 optimal weight:   10.0000
   chunk 58 optimal weight:    0.5980
   chunk 5 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 92 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 69 optimal weight:   10.0000
   chunk 88 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 124 GLN
B 159 HIS
B 478 ASN
D 116 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.141684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.115102 restraints weight = 19732.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.117896 restraints weight = 12083.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.119843 restraints weight = 8636.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.5473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9008  Z= 0.190
  Angle     :  0.747  10.367  12160  Z= 0.372
  Chirality :  0.047   0.215   1327
  Planarity :  0.004   0.040   1549
  Dihedral  :  8.252  63.148   1281
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.25), residues: 1065
  helix: -0.02 (0.20), residues: 653
  sheet: -1.68 (0.57), residues: 64
  loop : -1.57 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C  38 
 HIS   0.005   0.001   HIS B 526 
 PHE   0.024   0.002   PHE B 515 
 TYR   0.029   0.002   TYR B 495 
 ARG   0.009   0.000   ARG A 141 

===============================================================================
Job complete
usr+sys time: 2901.15 seconds
wall clock time: 52 minutes 49.27 seconds (3169.27 seconds total)