Starting phenix.real_space_refine
on Thu Mar 13 13:04:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pw9_20501/03_2025/6pw9_20501.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pw9_20501/03_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_20501/03_2025/6pw9_20501.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pw9_20501/03_2025/6pw9_20501.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pw9_20501/03_2025/6pw9_20501.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pw9_20501/03_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-5624/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: 5.01, per 1000 atoms: 0.57
  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: 2.15
  Conformation dependent library (CDL) restraints added in 951.7 milliseconds
  

  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: 0.83
  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: 2.37

  Time building geometry restraints manager: 2.53 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:             0.650
  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:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.620
  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:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.510
-------------------------------------------------------------------------------
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  : 0.969 
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: 0.2567
  time to fit residues: 105.9192
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  : 1.030 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 96 optimal weight:    9.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.4170 r_free = 0.4170 target = 0.147294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.120517 restraints weight = 19801.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.123441 restraints weight = 12073.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.125327 restraints weight = 8621.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.2813

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= 0.211
  Angle     :  0.760   9.814  12160  Z= 0.381
  Chirality :  0.047   0.317   1327
  Planarity :  0.005   0.066   1549
  Dihedral  : 10.292  62.473   1281
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  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: -2.75 (0.23), residues: 1065
  helix: -1.40 (0.19), residues: 647
  sheet: -1.96 (0.65), residues: 62
  loop : -2.34 (0.29), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 707 
 HIS   0.006   0.001   HIS A  95 
 PHE   0.018   0.002   PHE B 716 
 TYR   0.019   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
  256 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 249
  time to evaluate  : 1.045 
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: 0.7064 (m-30) cc_final: 0.6682 (t70)
REVERT: A   94 ASN cc_start: 0.7989 (m-40) cc_final: 0.7308 (t0)
REVERT: A   98 ASN cc_start: 0.8572 (p0) cc_final: 0.8351 (p0)
REVERT: A  138 TYR cc_start: 0.7867 (t80) cc_final: 0.7269 (t80)
REVERT: A  141 ARG cc_start: 0.7988 (mpp80) cc_final: 0.7721 (mpp80)
REVERT: A  146 ASP cc_start: 0.7278 (m-30) cc_final: 0.6451 (t70)
REVERT: A  148 HIS cc_start: 0.7526 (m90) cc_final: 0.7236 (m-70)
REVERT: B  166 MET cc_start: 0.3943 (ppp) cc_final: 0.3501 (ppp)
REVERT: B  278 LYS cc_start: 0.8194 (mttt) cc_final: 0.7674 (mmtm)
REVERT: B  358 LEU cc_start: 0.7052 (tp) cc_final: 0.6836 (pt)
REVERT: B  366 LYS cc_start: 0.7387 (pptt) cc_final: 0.6856 (tmtt)
REVERT: B  490 GLU cc_start: 0.8428 (tp30) cc_final: 0.8187 (tp30)
REVERT: B  551 HIS cc_start: 0.8099 (t-90) cc_final: 0.7397 (t70)
REVERT: B  726 LEU cc_start: 0.7564 (pp) cc_final: 0.6546 (tp)
REVERT: B  734 LEU cc_start: 0.9025 (tt) cc_final: 0.8615 (pp)
REVERT: B  749 ASN cc_start: 0.8672 (m110) cc_final: 0.8428 (p0)
REVERT: B  803 MET cc_start: 0.8208 (tmm) cc_final: 0.7683 (tmm)
REVERT: C   12 MET cc_start: 0.8133 (tmm) cc_final: 0.7826 (tmm)
REVERT: C   98 MET cc_start: 0.8256 (mtp) cc_final: 0.7912 (mtm)
REVERT: C  101 ASN cc_start: 0.8745 (p0) cc_final: 0.8505 (p0)
REVERT: D   91 LYS cc_start: 0.8718 (tttp) cc_final: 0.8375 (mtmt)
REVERT: D   92 LYS cc_start: 0.8501 (mppt) cc_final: 0.7761 (tptt)
REVERT: D  106 ARG cc_start: 0.6899 (tmm-80) cc_final: 0.6670 (ttp80)
  outliers start: 7
  outliers final: 1
  residues processed: 255
  average time/residue: 0.2385
  time to fit residues: 82.0273
Evaluate side-chains
  183 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 182
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 36 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 84 optimal weight:    4.9990
   chunk 69 optimal weight:   10.0000
   chunk 42 optimal weight:    4.9990
   chunk 15 optimal weight:    9.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    3.3388

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 736 GLN
C   5 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.137160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.110128 restraints weight = 20795.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.112714 restraints weight = 12872.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.114463 restraints weight = 9352.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.4032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075   9008  Z= 0.347
  Angle     :  0.836  11.015  12160  Z= 0.434
  Chirality :  0.052   0.294   1327
  Planarity :  0.005   0.051   1549
  Dihedral  :  9.851  57.100   1281
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  5.95 %
    Favored  : 93.52 %
  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: -2.42 (0.24), residues: 1065
  helix: -1.13 (0.19), residues: 650
  sheet: -1.85 (0.68), residues: 55
  loop : -2.23 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP B 707 
 HIS   0.008   0.002   HIS A  95 
 PHE   0.027   0.003   PHE B 515 
 TYR   0.023   0.002   TYR B 349 
 ARG   0.007   0.001   ARG B 782 

*********************** 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
  244 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 239
  time to evaluate  : 0.982 
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   53 ASP cc_start: 0.7250 (m-30) cc_final: 0.6600 (t70)
REVERT: A   94 ASN cc_start: 0.8031 (m-40) cc_final: 0.7101 (t0)
REVERT: A   98 ASN cc_start: 0.8597 (p0) cc_final: 0.8376 (p0)
REVERT: A  138 TYR cc_start: 0.7962 (t80) cc_final: 0.7660 (t80)
REVERT: A  141 ARG cc_start: 0.8083 (mpp80) cc_final: 0.7755 (mpp80)
REVERT: A  146 ASP cc_start: 0.7510 (m-30) cc_final: 0.6958 (m-30)
REVERT: A  148 HIS cc_start: 0.7617 (m90) cc_final: 0.7359 (m-70)
REVERT: B  158 TYR cc_start: 0.7697 (m-80) cc_final: 0.7004 (m-80)
REVERT: B  166 MET cc_start: 0.3864 (ppp) cc_final: 0.3578 (ppp)
REVERT: B  191 GLU cc_start: 0.7719 (tp30) cc_final: 0.7338 (tp30)
REVERT: B  291 LEU cc_start: 0.8676 (tp) cc_final: 0.8475 (tp)
REVERT: B  358 LEU cc_start: 0.7487 (tp) cc_final: 0.7125 (pt)
REVERT: B  366 LYS cc_start: 0.7262 (pptt) cc_final: 0.6951 (tmtt)
REVERT: B  490 GLU cc_start: 0.8589 (tp30) cc_final: 0.8339 (tp30)
REVERT: B  551 HIS cc_start: 0.8493 (t-90) cc_final: 0.7894 (t-90)
REVERT: B  749 ASN cc_start: 0.8768 (m110) cc_final: 0.8366 (p0)
REVERT: B  803 MET cc_start: 0.8446 (tmm) cc_final: 0.7868 (tmm)
REVERT: C   12 MET cc_start: 0.8549 (tmm) cc_final: 0.8100 (tmm)
REVERT: C  134 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8275 (mm-30)
REVERT: D   91 LYS cc_start: 0.8664 (tttp) cc_final: 0.8290 (mtmt)
REVERT: D   92 LYS cc_start: 0.8569 (mppt) cc_final: 0.7861 (tptt)
REVERT: D  106 ARG cc_start: 0.7089 (tmm-80) cc_final: 0.6757 (ttp80)
REVERT: D  115 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7266 (mp0)
  outliers start: 5
  outliers final: 1
  residues processed: 242
  average time/residue: 0.2247
  time to fit residues: 73.7574
Evaluate side-chains
  184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 183
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 18 optimal weight:    8.9990
   chunk 55 optimal weight:    1.9990
   chunk 14 optimal weight:   20.0000
   chunk 35 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 159 HIS
B 197 ASN
B 478 ASN
B 509 HIS
C  71 HIS
C 110 HIS
D 116 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.140827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.113449 restraints weight = 20205.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.116129 restraints weight = 12425.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.117992 restraints weight = 8984.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
moved from start:          0.4331

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= 0.188
  Angle     :  0.716   8.141  12160  Z= 0.361
  Chirality :  0.047   0.238   1327
  Planarity :  0.004   0.070   1549
  Dihedral  :  9.267  58.374   1281
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  4.68 %
    Favored  : 94.90 %
  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: -1.90 (0.24), residues: 1065
  helix: -0.71 (0.19), residues: 651
  sheet: -1.53 (0.80), residues: 41
  loop : -2.05 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 707 
 HIS   0.008   0.001   HIS B 526 
 PHE   0.019   0.002   PHE B 716 
 TYR   0.024   0.002   TYR B 154 
 ARG   0.004   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
  244 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 240
  time to evaluate  : 1.331 
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: A   53 ASP cc_start: 0.7132 (m-30) cc_final: 0.6796 (t70)
REVERT: A   94 ASN cc_start: 0.8154 (m-40) cc_final: 0.7240 (t0)
REVERT: A   98 ASN cc_start: 0.8566 (p0) cc_final: 0.8323 (p0)
REVERT: A  138 TYR cc_start: 0.7953 (t80) cc_final: 0.7726 (t80)
REVERT: A  141 ARG cc_start: 0.7989 (mpp80) cc_final: 0.7758 (mpp80)
REVERT: A  146 ASP cc_start: 0.7326 (m-30) cc_final: 0.6873 (m-30)
REVERT: B  166 MET cc_start: 0.3723 (ppp) cc_final: 0.3155 (ppp)
REVERT: B  191 GLU cc_start: 0.7868 (tp30) cc_final: 0.7496 (tp30)
REVERT: B  224 LEU cc_start: 0.8003 (tt) cc_final: 0.7761 (tt)
REVERT: B  291 LEU cc_start: 0.8627 (tp) cc_final: 0.8367 (tp)
REVERT: B  366 LYS cc_start: 0.7298 (pptt) cc_final: 0.6802 (tmtt)
REVERT: B  430 TRP cc_start: 0.6948 (m100) cc_final: 0.6651 (m100)
REVERT: B  490 GLU cc_start: 0.8472 (tp30) cc_final: 0.8269 (tp30)
REVERT: B  523 PHE cc_start: 0.8489 (t80) cc_final: 0.8039 (t80)
REVERT: B  551 HIS cc_start: 0.8413 (t-90) cc_final: 0.7800 (t-90)
REVERT: B  710 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7576 (mp0)
REVERT: B  728 ASP cc_start: 0.7870 (p0) cc_final: 0.7606 (p0)
REVERT: B  734 LEU cc_start: 0.9083 (tt) cc_final: 0.8874 (pp)
REVERT: B  803 MET cc_start: 0.8274 (tmm) cc_final: 0.7683 (tmm)
REVERT: B  827 ASN cc_start: 0.8076 (t0) cc_final: 0.7782 (t0)
REVERT: C    7 ARG cc_start: 0.8267 (mmt-90) cc_final: 0.8039 (mmt180)
REVERT: C   12 MET cc_start: 0.8411 (tmm) cc_final: 0.7930 (tmm)
REVERT: C   15 GLN cc_start: 0.8238 (pt0) cc_final: 0.8019 (pt0)
REVERT: C   91 MET cc_start: 0.8143 (tpp) cc_final: 0.7777 (tpp)
REVERT: C  134 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8234 (mm-30)
REVERT: D   91 LYS cc_start: 0.8694 (tttp) cc_final: 0.8283 (mtmt)
REVERT: D   92 LYS cc_start: 0.8673 (mppt) cc_final: 0.7915 (tptt)
  outliers start: 4
  outliers final: 0
  residues processed: 243
  average time/residue: 0.2254
  time to fit residues: 74.3412
Evaluate side-chains
  189 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 102 optimal weight:    7.9990
   chunk 97 optimal weight:    7.9990
   chunk 26 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0070
   chunk 13 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    1.8004

-------------------------------------------------------------------------------
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 196 GLN
B 478 ASN
B 736 GLN
D 116 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.139456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.111946 restraints weight = 20341.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.114581 restraints weight = 12605.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.116279 restraints weight = 9194.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.4653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9008  Z= 0.228
  Angle     :  0.731   8.185  12160  Z= 0.372
  Chirality :  0.047   0.235   1327
  Planarity :  0.004   0.040   1549
  Dihedral  :  9.142  57.422   1281
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  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: -1.76 (0.24), residues: 1065
  helix: -0.59 (0.19), residues: 653
  sheet: -1.63 (0.78), residues: 41
  loop : -1.99 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C  38 
 HIS   0.007   0.001   HIS B 526 
 PHE   0.021   0.002   PHE B 716 
 TYR   0.017   0.002   TYR B 158 
 ARG   0.008   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
  239 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 1.034 
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   53 ASP cc_start: 0.7166 (m-30) cc_final: 0.6872 (t70)
REVERT: A   90 THR cc_start: 0.7699 (m) cc_final: 0.7317 (m)
REVERT: A   94 ASN cc_start: 0.8141 (m-40) cc_final: 0.7580 (m110)
REVERT: A  141 ARG cc_start: 0.7993 (mpp80) cc_final: 0.7755 (mpp80)
REVERT: A  146 ASP cc_start: 0.7364 (m-30) cc_final: 0.6905 (m-30)
REVERT: B  166 MET cc_start: 0.3956 (ppp) cc_final: 0.3695 (ppp)
REVERT: B  173 GLU cc_start: 0.7989 (pp20) cc_final: 0.7765 (pp20)
REVERT: B  191 GLU cc_start: 0.7972 (tp30) cc_final: 0.7741 (tp30)
REVERT: B  224 LEU cc_start: 0.8102 (tt) cc_final: 0.7843 (tt)
REVERT: B  366 LYS cc_start: 0.7517 (pptt) cc_final: 0.6893 (tmtt)
REVERT: B  490 GLU cc_start: 0.8502 (tp30) cc_final: 0.8241 (tp30)
REVERT: B  523 PHE cc_start: 0.8374 (t80) cc_final: 0.8025 (t80)
REVERT: B  551 HIS cc_start: 0.8405 (t-90) cc_final: 0.8030 (t-90)
REVERT: B  710 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7614 (mp0)
REVERT: B  738 MET cc_start: 0.8514 (mmm) cc_final: 0.8209 (mmm)
REVERT: B  803 MET cc_start: 0.8416 (tmm) cc_final: 0.7813 (tmm)
REVERT: B  827 ASN cc_start: 0.7973 (t0) cc_final: 0.7685 (t0)
REVERT: C   46 GLU cc_start: 0.8026 (pt0) cc_final: 0.7689 (pt0)
REVERT: C  134 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8225 (mm-30)
REVERT: D   91 LYS cc_start: 0.8727 (tttp) cc_final: 0.8307 (mtmt)
REVERT: D   92 LYS cc_start: 0.8683 (mppt) cc_final: 0.7948 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 0.2224
  time to fit residues: 72.1766
Evaluate side-chains
  185 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 50 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 37 optimal weight:    0.1980
   chunk 79 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 61 optimal weight:    5.9990
   chunk 52 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 478 ASN
C  71 HIS
D 116 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.141564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.114547 restraints weight = 19948.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.117282 restraints weight = 12124.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.119158 restraints weight = 8681.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.4802

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= 0.184
  Angle     :  0.719   9.804  12160  Z= 0.357
  Chirality :  0.046   0.223   1327
  Planarity :  0.004   0.043   1549
  Dihedral  :  8.835  56.832   1281
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.14 %
    Favored  : 95.75 %
  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: -1.47 (0.25), residues: 1065
  helix: -0.37 (0.20), residues: 656
  sheet: -1.75 (0.71), residues: 49
  loop : -1.81 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C  38 
 HIS   0.007   0.001   HIS B 526 
 PHE   0.022   0.002   PHE B 515 
 TYR   0.015   0.001   TYR B 495 
 ARG   0.007   0.000   ARG B 137 

*********************** 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
  249 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 248
  time to evaluate  : 1.007 
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   90 THR cc_start: 0.7737 (m) cc_final: 0.7401 (m)
REVERT: A  141 ARG cc_start: 0.8021 (mpp80) cc_final: 0.7785 (mpp80)
REVERT: A  146 ASP cc_start: 0.7381 (m-30) cc_final: 0.6940 (m-30)
REVERT: B  159 HIS cc_start: 0.8238 (t-90) cc_final: 0.7967 (t-170)
REVERT: B  166 MET cc_start: 0.3887 (ppp) cc_final: 0.3681 (ppp)
REVERT: B  191 GLU cc_start: 0.7573 (tp30) cc_final: 0.7305 (tp30)
REVERT: B  224 LEU cc_start: 0.8180 (tt) cc_final: 0.7894 (tt)
REVERT: B  291 LEU cc_start: 0.8606 (tp) cc_final: 0.8268 (tp)
REVERT: B  366 LYS cc_start: 0.7461 (pptt) cc_final: 0.6863 (tmtt)
REVERT: B  430 TRP cc_start: 0.6988 (m100) cc_final: 0.6758 (m100)
REVERT: B  450 LYS cc_start: 0.8034 (ttpt) cc_final: 0.7714 (ttmm)
REVERT: B  490 GLU cc_start: 0.8441 (tp30) cc_final: 0.8212 (tp30)
REVERT: B  523 PHE cc_start: 0.8370 (t80) cc_final: 0.8067 (t80)
REVERT: B  551 HIS cc_start: 0.8374 (t-90) cc_final: 0.8014 (t-90)
REVERT: B  710 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7539 (mp0)
REVERT: B  728 ASP cc_start: 0.7653 (p0) cc_final: 0.6626 (t0)
REVERT: B  803 MET cc_start: 0.8276 (tmm) cc_final: 0.7657 (tmm)
REVERT: B  827 ASN cc_start: 0.8046 (t0) cc_final: 0.7769 (t0)
REVERT: C    7 ARG cc_start: 0.8161 (mmt-90) cc_final: 0.7935 (mmt180)
REVERT: C  134 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8182 (mm-30)
REVERT: D   91 LYS cc_start: 0.8692 (tttp) cc_final: 0.8275 (mtmt)
REVERT: D   92 LYS cc_start: 0.8693 (mppt) cc_final: 0.7936 (tptt)
  outliers start: 1
  outliers final: 1
  residues processed: 248
  average time/residue: 0.2502
  time to fit residues: 85.2751
Evaluate side-chains
  189 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 188
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 47 optimal weight:    8.9990
   chunk 35 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 70 optimal weight:    5.9990
   chunk 61 optimal weight:    0.0570
   chunk 63 optimal weight:    0.0980
   chunk 7 optimal weight:    7.9990
   chunk 93 optimal weight:    0.8980
   overall best weight:    1.6102

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.4076 r_free = 0.4076 target = 0.140370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.113329 restraints weight = 20288.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.116058 restraints weight = 12430.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.117894 restraints weight = 8888.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.5053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9008  Z= 0.218
  Angle     :  0.738   9.660  12160  Z= 0.371
  Chirality :  0.047   0.226   1327
  Planarity :  0.004   0.040   1549
  Dihedral  :  8.851  59.399   1281
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  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: -0.30 (0.20), residues: 657
  sheet: -1.77 (0.60), residues: 65
  loop : -1.68 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 486 
 HIS   0.007   0.001   HIS B 526 
 PHE   0.024   0.002   PHE B 515 
 TYR   0.030   0.002   TYR B 154 
 ARG   0.005   0.000   ARG D 106 

*********************** 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
  242 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 1.844 
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  141 ARG cc_start: 0.8120 (mpp80) cc_final: 0.7819 (mpp80)
REVERT: A  146 ASP cc_start: 0.7494 (m-30) cc_final: 0.7060 (m-30)
REVERT: B  166 MET cc_start: 0.4058 (ppp) cc_final: 0.3766 (ppp)
REVERT: B  173 GLU cc_start: 0.7875 (pp20) cc_final: 0.7628 (pp20)
REVERT: B  191 GLU cc_start: 0.7760 (tp30) cc_final: 0.7509 (tp30)
REVERT: B  224 LEU cc_start: 0.8244 (tt) cc_final: 0.7993 (tt)
REVERT: B  291 LEU cc_start: 0.8648 (tp) cc_final: 0.8278 (tp)
REVERT: B  366 LYS cc_start: 0.7479 (pptt) cc_final: 0.6811 (tmtt)
REVERT: B  450 LYS cc_start: 0.8047 (ttpt) cc_final: 0.7714 (ttmm)
REVERT: B  490 GLU cc_start: 0.8503 (tp30) cc_final: 0.8244 (tp30)
REVERT: B  510 GLU cc_start: 0.8139 (pm20) cc_final: 0.7536 (pm20)
REVERT: B  523 PHE cc_start: 0.8472 (t80) cc_final: 0.8229 (t80)
REVERT: B  551 HIS cc_start: 0.8446 (t-90) cc_final: 0.8097 (t-90)
REVERT: B  710 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7650 (mp0)
REVERT: B  726 LEU cc_start: 0.7758 (pp) cc_final: 0.6695 (tp)
REVERT: B  737 GLU cc_start: 0.7850 (mp0) cc_final: 0.7584 (mp0)
REVERT: B  738 MET cc_start: 0.8598 (mmm) cc_final: 0.8386 (mmm)
REVERT: B  803 MET cc_start: 0.8314 (tmm) cc_final: 0.7698 (tmm)
REVERT: B  827 ASN cc_start: 0.8106 (t0) cc_final: 0.7842 (t0)
REVERT: C  134 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8209 (mm-30)
REVERT: D   91 LYS cc_start: 0.8633 (tttp) cc_final: 0.8308 (mtmt)
REVERT: D   92 LYS cc_start: 0.8706 (mppt) cc_final: 0.8095 (tptt)
REVERT: D   96 GLU cc_start: 0.8787 (tp30) cc_final: 0.8573 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.2918
  time to fit residues: 96.7801
Evaluate side-chains
  188 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 84 optimal weight:    0.5980
   chunk 81 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 65 optimal weight:    0.8980
   chunk 14 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 151 GLN
B 327 ASN
B 478 ASN
C  71 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.136149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.109232 restraints weight = 20832.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.111798 restraints weight = 12917.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.113531 restraints weight = 9356.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.5453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9008  Z= 0.261
  Angle     :  0.781   9.097  12160  Z= 0.397
  Chirality :  0.049   0.231   1327
  Planarity :  0.004   0.040   1549
  Dihedral  :  8.831  64.428   1281
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  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: -1.28 (0.25), residues: 1065
  helix: -0.22 (0.20), residues: 656
  sheet: -2.03 (0.58), residues: 65
  loop : -1.63 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP B 486 
 HIS   0.008   0.001   HIS B 526 
 PHE   0.026   0.002   PHE B 716 
 TYR   0.021   0.002   TYR B 495 
 ARG   0.005   0.001   ARG C  96 

*********************** 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
  245 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 1.082 
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   91 LYS cc_start: 0.8676 (tttm) cc_final: 0.8184 (tptp)
REVERT: A   94 ASN cc_start: 0.8091 (m110) cc_final: 0.7609 (m110)
REVERT: A  141 ARG cc_start: 0.8192 (mpp80) cc_final: 0.7834 (mpp80)
REVERT: A  146 ASP cc_start: 0.7598 (m-30) cc_final: 0.7120 (m-30)
REVERT: B  191 GLU cc_start: 0.7867 (tp30) cc_final: 0.7651 (tp30)
REVERT: B  291 LEU cc_start: 0.8795 (tp) cc_final: 0.8447 (tp)
REVERT: B  366 LYS cc_start: 0.7360 (pptt) cc_final: 0.6785 (tmtt)
REVERT: B  450 LYS cc_start: 0.8079 (ttpt) cc_final: 0.7767 (ttmm)
REVERT: B  490 GLU cc_start: 0.8569 (tp30) cc_final: 0.8272 (tp30)
REVERT: B  523 PHE cc_start: 0.8484 (t80) cc_final: 0.8173 (t80)
REVERT: B  710 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7806 (mp0)
REVERT: B  726 LEU cc_start: 0.7835 (pp) cc_final: 0.6753 (tp)
REVERT: B  728 ASP cc_start: 0.7797 (p0) cc_final: 0.7017 (t0)
REVERT: B  737 GLU cc_start: 0.7925 (mp0) cc_final: 0.7559 (mp0)
REVERT: B  803 MET cc_start: 0.8357 (tmm) cc_final: 0.7726 (tmm)
REVERT: B  827 ASN cc_start: 0.8141 (t0) cc_final: 0.7911 (t0)
REVERT: C   12 MET cc_start: 0.8629 (tmm) cc_final: 0.8248 (tmm)
REVERT: C  134 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8272 (tp30)
REVERT: D   91 LYS cc_start: 0.8748 (tttp) cc_final: 0.8330 (mtmt)
REVERT: D   92 LYS cc_start: 0.8953 (mppt) cc_final: 0.8072 (tptt)
REVERT: D  125 ILE cc_start: 0.7916 (mt) cc_final: 0.7714 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 245
  average time/residue: 0.2264
  time to fit residues: 76.1185
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  : 1.082 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 70 optimal weight:    0.0970
   chunk 20 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 80 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
B 124 GLN
B 159 HIS
B 478 ASN
B 739 ASN
D 116 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.138380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.111430 restraints weight = 20370.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.114158 restraints weight = 12419.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.115916 restraints weight = 8911.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.5523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9008  Z= 0.204
  Angle     :  0.744   8.466  12160  Z= 0.372
  Chirality :  0.047   0.222   1327
  Planarity :  0.004   0.045   1549
  Dihedral  :  8.624  62.712   1281
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  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: -1.14 (0.25), residues: 1065
  helix: -0.13 (0.20), residues: 655
  sheet: -2.02 (0.58), residues: 65
  loop : -1.52 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 486 
 HIS   0.006   0.001   HIS B 526 
 PHE   0.024   0.002   PHE B 515 
 TYR   0.024   0.002   TYR B 154 
 ARG   0.006   0.000   ARG C  96 

*********************** 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
  237 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 1.093 
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    8 LEU cc_start: 0.6306 (mt) cc_final: 0.5855 (mt)
REVERT: A   91 LYS cc_start: 0.8808 (tttm) cc_final: 0.8439 (tptp)
REVERT: A   94 ASN cc_start: 0.8109 (m110) cc_final: 0.7691 (t0)
REVERT: A  141 ARG cc_start: 0.8200 (mpp80) cc_final: 0.7886 (mpp80)
REVERT: A  146 ASP cc_start: 0.7559 (m-30) cc_final: 0.7065 (m-30)
REVERT: B  191 GLU cc_start: 0.7728 (tp30) cc_final: 0.7441 (tp30)
REVERT: B  291 LEU cc_start: 0.8686 (tp) cc_final: 0.8211 (tp)
REVERT: B  366 LYS cc_start: 0.7390 (pptt) cc_final: 0.6788 (tmtt)
REVERT: B  450 LYS cc_start: 0.8101 (ttpt) cc_final: 0.7641 (ttmm)
REVERT: B  490 GLU cc_start: 0.8500 (tp30) cc_final: 0.8250 (tp30)
REVERT: B  523 PHE cc_start: 0.8409 (t80) cc_final: 0.8125 (t80)
REVERT: B  551 HIS cc_start: 0.8466 (t-90) cc_final: 0.8008 (t70)
REVERT: B  710 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7759 (mp0)
REVERT: B  726 LEU cc_start: 0.7833 (pp) cc_final: 0.6838 (tp)
REVERT: B  728 ASP cc_start: 0.7769 (p0) cc_final: 0.6955 (t0)
REVERT: B  738 MET cc_start: 0.8682 (mmm) cc_final: 0.8342 (mmm)
REVERT: B  803 MET cc_start: 0.8292 (tmm) cc_final: 0.7684 (tmm)
REVERT: C   91 MET cc_start: 0.8066 (tpp) cc_final: 0.7856 (tpp)
REVERT: C  134 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8240 (tp30)
REVERT: D   91 LYS cc_start: 0.8671 (tttp) cc_final: 0.8239 (mtmt)
REVERT: D   92 LYS cc_start: 0.8782 (mppt) cc_final: 0.8115 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 237
  average time/residue: 0.2279
  time to fit residues: 74.2855
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  : 0.986 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 16 optimal weight:    0.0770
   chunk 60 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 51 optimal weight:    9.9990
   chunk 58 optimal weight:    3.9990
   chunk 72 optimal weight:    0.6980
   chunk 80 optimal weight:    0.0770
   chunk 92 optimal weight:    5.9990
   chunk 105 optimal weight:    5.9990
   chunk 94 optimal weight:    0.7980
   overall best weight:    0.4496

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.141814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.114943 restraints weight = 19962.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.117668 restraints weight = 12278.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.119581 restraints weight = 8828.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.5583

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= 0.174
  Angle     :  0.734   8.711  12160  Z= 0.361
  Chirality :  0.046   0.211   1327
  Planarity :  0.004   0.052   1549
  Dihedral  :  8.334  60.047   1281
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  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: -1.01 (0.25), residues: 1065
  helix:  0.01 (0.20), residues: 654
  sheet: -1.61 (0.65), residues: 55
  loop : -1.64 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C  38 
 HIS   0.006   0.001   HIS D 116 
 PHE   0.020   0.002   PHE C 102 
 TYR   0.023   0.002   TYR B 154 
 ARG   0.004   0.000   ARG B 137 

********************** 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
  246 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 0.962 
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    8 LEU cc_start: 0.6411 (mt) cc_final: 0.5957 (mt)
REVERT: A   91 LYS cc_start: 0.8742 (tttm) cc_final: 0.8369 (tptp)
REVERT: A   94 ASN cc_start: 0.7969 (m110) cc_final: 0.7754 (t0)
REVERT: A  141 ARG cc_start: 0.8178 (mpp80) cc_final: 0.7884 (mpp80)
REVERT: A  146 ASP cc_start: 0.7492 (m-30) cc_final: 0.7015 (m-30)
REVERT: B  191 GLU cc_start: 0.7727 (tp30) cc_final: 0.7300 (tp30)
REVERT: B  291 LEU cc_start: 0.8678 (tp) cc_final: 0.8237 (tp)
REVERT: B  366 LYS cc_start: 0.7341 (pptt) cc_final: 0.6786 (tmtt)
REVERT: B  450 LYS cc_start: 0.7949 (ttpt) cc_final: 0.7563 (ttmm)
REVERT: B  523 PHE cc_start: 0.8308 (t80) cc_final: 0.8092 (t80)
REVERT: B  551 HIS cc_start: 0.8375 (t-90) cc_final: 0.7954 (t70)
REVERT: B  726 LEU cc_start: 0.7837 (pp) cc_final: 0.6862 (tp)
REVERT: B  728 ASP cc_start: 0.7820 (p0) cc_final: 0.7006 (t0)
REVERT: B  803 MET cc_start: 0.8233 (tmm) cc_final: 0.7637 (tmm)
REVERT: C   59 LYS cc_start: 0.8743 (tttp) cc_final: 0.8219 (tttp)
REVERT: C  134 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8244 (tp30)
REVERT: D   91 LYS cc_start: 0.8592 (tttp) cc_final: 0.8203 (mtmt)
REVERT: D   92 LYS cc_start: 0.8744 (mppt) cc_final: 0.8079 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 246
  average time/residue: 0.2211
  time to fit residues: 75.0475
Evaluate side-chains
  188 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 99 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 40 optimal weight:    8.9990
   chunk 92 optimal weight:   10.0000
   chunk 60 optimal weight:    2.9990
   chunk 69 optimal weight:   10.0000
   chunk 88 optimal weight:    5.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
B 124 GLN
B 327 ASN
B 478 ASN
** B 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 116 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.136087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.109359 restraints weight = 20359.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.111885 restraints weight = 12799.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.113573 restraints weight = 9372.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.5816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   9008  Z= 0.288
  Angle     :  0.811   9.667  12160  Z= 0.411
  Chirality :  0.051   0.226   1327
  Planarity :  0.005   0.048   1549
  Dihedral  :  8.579  66.273   1281
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  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: -1.09 (0.25), residues: 1065
  helix: -0.11 (0.20), residues: 654
  sheet: -1.94 (0.58), residues: 66
  loop : -1.46 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP B 486 
 HIS   0.006   0.001   HIS B 526 
 PHE   0.024   0.002   PHE B 716 
 TYR   0.037   0.003   TYR B 495 
 ARG   0.005   0.001   ARG B 137 

===============================================================================
Job complete
usr+sys time: 3211.19 seconds
wall clock time: 57 minutes 38.22 seconds (3458.22 seconds total)