Starting phenix.real_space_refine
on Tue Mar  3 22:01:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pw9_20501/03_2026/6pw9_20501.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pw9_20501/03_2026/6pw9_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pw9_20501/03_2026/6pw9_20501.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pw9_20501/03_2026/6pw9_20501.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6pw9_20501/03_2026/6pw9_20501.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pw9_20501/03_2026/6pw9_20501.map"
  }
  resolution = 4.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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, 'ASP:plan': 2, 'ARG:plan': 3}
          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: {'ARG:plan': 1, 'GLN:plan1': 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: 2.24, per 1000 atoms: 0.25
  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: 0.68
  Conformation dependent library (CDL) restraints added in 276.3 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: 0.20
  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: 1.12

  Time building geometry restraints manager: 0.90 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:             0.470
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.410
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.440
-------------------------------------------------------------------------------
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= 0.506
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.007   0.001   ARG B 714 
 TYR   0.042   0.003   TYR B 565 
 PHE   0.030   0.003   PHE B 716 
 TRP   0.047   0.003   TRP B 707 
 HIS   0.007   0.002   HIS A 148 

Details of bonding type rmsd
  covalent geometry    : bond        0.00743 ( 9008)
  covalent geometry    : angle       1.22562 (12160)
  hydrogen bonds       : bond        0.12168 (  483)
  hydrogen bonds       : angle       6.94602 ( 1428)

*********************** 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  : 0.343 
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: 0.1095
  time to fit residues: 45.5677
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  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:   10.0000
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    8.9990
   overall best weight:    1.6382

-------------------------------------------------------------------------------
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 = 0.4149 r_free = 0.4149 target = 0.145504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.118641 restraints weight = 19929.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.121551 restraints weight = 12213.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.123492 restraints weight = 8715.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.124825 restraints weight = 6969.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.125423 restraints weight = 6001.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.2895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9008  Z= 0.155
  Angle     :  0.767   9.581  12160  Z= 0.386
  Chirality :  0.047   0.254   1327
  Planarity :  0.005   0.067   1549
  Dihedral  : 10.199  61.589   1281
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  5.84 %
    Favored  : 93.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.71 (0.23), residues: 1065
  helix: -1.36 (0.19), residues: 647
  sheet: -1.99 (0.65), residues: 62
  loop : -2.31 (0.29), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 118 
 TYR   0.018   0.002   TYR A  73 
 PHE   0.019   0.002   PHE B 716 
 TRP   0.031   0.002   TRP B 707 
 HIS   0.007   0.001   HIS B 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 9008)
  covalent geometry    : angle       0.76744 (12160)
  hydrogen bonds       : bond        0.04155 (  483)
  hydrogen bonds       : angle       5.18100 ( 1428)

*********************** 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
  258 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 251
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 SER cc_start: 0.8447 (t) cc_final: 0.8065 (p)
REVERT: A   53 ASP cc_start: 0.7006 (m-30) cc_final: 0.6712 (t70)
REVERT: A   94 ASN cc_start: 0.7992 (m-40) cc_final: 0.7291 (t0)
REVERT: A   98 ASN cc_start: 0.8562 (p0) cc_final: 0.8354 (p0)
REVERT: A  138 TYR cc_start: 0.7875 (t80) cc_final: 0.7266 (t80)
REVERT: A  141 ARG cc_start: 0.7987 (mpp80) cc_final: 0.7706 (mpp80)
REVERT: A  146 ASP cc_start: 0.7292 (m-30) cc_final: 0.6462 (t70)
REVERT: A  148 HIS cc_start: 0.7496 (m90) cc_final: 0.7242 (m-70)
REVERT: B  191 GLU cc_start: 0.7766 (pp20) cc_final: 0.7442 (tp30)
REVERT: B  278 LYS cc_start: 0.8224 (mttt) cc_final: 0.7706 (mmtm)
REVERT: B  366 LYS cc_start: 0.7395 (pptt) cc_final: 0.6848 (tmtt)
REVERT: B  490 GLU cc_start: 0.8468 (tp30) cc_final: 0.8237 (tp30)
REVERT: B  551 HIS cc_start: 0.8129 (t-90) cc_final: 0.7407 (t70)
REVERT: B  672 ILE cc_start: 0.7196 (pt) cc_final: 0.6959 (pt)
REVERT: B  726 LEU cc_start: 0.7518 (pp) cc_final: 0.6511 (tp)
REVERT: B  734 LEU cc_start: 0.8998 (tt) cc_final: 0.8591 (pp)
REVERT: B  749 ASN cc_start: 0.8633 (m110) cc_final: 0.8413 (p0)
REVERT: B  803 MET cc_start: 0.8244 (tmm) cc_final: 0.7728 (tmm)
REVERT: C   12 MET cc_start: 0.8172 (tmm) cc_final: 0.7882 (tmm)
REVERT: C   98 MET cc_start: 0.8238 (mtp) cc_final: 0.8008 (mtp)
REVERT: C  101 ASN cc_start: 0.8736 (p0) cc_final: 0.8506 (p0)
REVERT: D   91 LYS cc_start: 0.8642 (tttp) cc_final: 0.8295 (mtmt)
REVERT: D   92 LYS cc_start: 0.8481 (mppt) cc_final: 0.7760 (tptt)
  outliers start: 7
  outliers final: 2
  residues processed: 257
  average time/residue: 0.1030
  time to fit residues: 35.5216
Evaluate side-chains
  186 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 184
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 101 optimal weight:   20.0000
   chunk 25 optimal weight:    7.9990
   chunk 1 optimal weight:    7.9990
   chunk 96 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 86 optimal weight:    0.0050
   chunk 65 optimal weight:    5.9990
   chunk 39 optimal weight:    8.9990
   chunk 12 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 94 optimal weight:    8.9990
   overall best weight:    3.6002

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

Flipped N/Q/H residues before XYZ refinement:
A  18 GLN
** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 478 ASN
B 736 GLN
C   5 ASN
C  71 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.135613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.108822 restraints weight = 20589.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.111296 restraints weight = 12750.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.112914 restraints weight = 9335.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.114049 restraints weight = 7643.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.114816 restraints weight = 6695.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.4208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.076   9008  Z= 0.250
  Angle     :  0.860  11.509  12160  Z= 0.447
  Chirality :  0.053   0.304   1327
  Planarity :  0.005   0.050   1549
  Dihedral  :  9.969  57.951   1281
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  7.12 %
    Favored  : 92.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.45 (0.23), residues: 1065
  helix: -1.17 (0.19), residues: 652
  sheet: -1.68 (0.75), residues: 41
  loop : -2.25 (0.29), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 106 
 TYR   0.025   0.003   TYR B 349 
 PHE   0.028   0.003   PHE B 515 
 TRP   0.023   0.003   TRP B 707 
 HIS   0.010   0.002   HIS B 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00571 ( 9008)
  covalent geometry    : angle       0.86004 (12160)
  hydrogen bonds       : bond        0.05105 (  483)
  hydrogen bonds       : angle       5.28467 ( 1428)

*********************** 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  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 ASP cc_start: 0.7335 (m-30) cc_final: 0.6789 (t0)
REVERT: A   94 ASN cc_start: 0.8027 (m-40) cc_final: 0.7283 (t0)
REVERT: A   98 ASN cc_start: 0.8549 (p0) cc_final: 0.8304 (p0)
REVERT: A  138 TYR cc_start: 0.7972 (t80) cc_final: 0.7680 (t80)
REVERT: A  141 ARG cc_start: 0.8147 (mpp80) cc_final: 0.7797 (mpp80)
REVERT: A  146 ASP cc_start: 0.7495 (m-30) cc_final: 0.6986 (m-30)
REVERT: A  148 HIS cc_start: 0.7622 (m90) cc_final: 0.7350 (m-70)
REVERT: B  166 MET cc_start: 0.3818 (ppp) cc_final: 0.3377 (ppp)
REVERT: B  366 LYS cc_start: 0.7264 (pptt) cc_final: 0.6918 (tmtt)
REVERT: B  447 LYS cc_start: 0.8304 (mttt) cc_final: 0.8066 (mttt)
REVERT: B  490 GLU cc_start: 0.8621 (tp30) cc_final: 0.8345 (tp30)
REVERT: B  551 HIS cc_start: 0.8517 (t-90) cc_final: 0.7910 (t-90)
REVERT: B  734 LEU cc_start: 0.9196 (tt) cc_final: 0.8745 (tt)
REVERT: B  749 ASN cc_start: 0.8727 (m110) cc_final: 0.8336 (p0)
REVERT: B  803 MET cc_start: 0.8461 (tmm) cc_final: 0.7874 (tmm)
REVERT: C    7 ARG cc_start: 0.8314 (mmt-90) cc_final: 0.8042 (mmt180)
REVERT: C   12 MET cc_start: 0.8790 (tmm) cc_final: 0.8302 (tmm)
REVERT: C  134 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8233 (mm-30)
REVERT: C  137 TYR cc_start: 0.7703 (t80) cc_final: 0.7490 (t80)
REVERT: D   91 LYS cc_start: 0.8648 (tttp) cc_final: 0.8290 (mtmt)
REVERT: D   92 LYS cc_start: 0.8550 (mppt) cc_final: 0.7857 (tptt)
  outliers start: 5
  outliers final: 1
  residues processed: 243
  average time/residue: 0.0981
  time to fit residues: 32.3098
Evaluate side-chains
  178 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 177
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 77 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 100 optimal weight:    7.9990
   chunk 40 optimal weight:    7.9990
   chunk 8 optimal weight:    0.7980
   chunk 53 optimal weight:    0.5980
   chunk 93 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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
B 736 GLN
C  71 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 = 0.4086 r_free = 0.4086 target = 0.140862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.113384 restraints weight = 20373.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.116127 restraints weight = 12517.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.117982 restraints weight = 9028.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.119058 restraints weight = 7290.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.119961 restraints weight = 6372.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.4388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9008  Z= 0.137
  Angle     :  0.745  10.607  12160  Z= 0.373
  Chirality :  0.048   0.243   1327
  Planarity :  0.004   0.055   1549
  Dihedral  :  9.416  59.263   1281
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  4.78 %
    Favored  : 95.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.98 (0.24), residues: 1065
  helix: -0.77 (0.19), residues: 651
  sheet: -1.54 (0.80), residues: 41
  loop : -2.09 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 106 
 TYR   0.026   0.002   TYR B 154 
 PHE   0.019   0.002   PHE B 716 
 TRP   0.016   0.002   TRP B 707 
 HIS   0.009   0.001   HIS B 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9008)
  covalent geometry    : angle       0.74481 (12160)
  hydrogen bonds       : bond        0.03921 (  483)
  hydrogen bonds       : angle       4.80800 ( 1428)

*********************** 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
  238 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 236
  time to evaluate  : 0.347 
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   53 ASP cc_start: 0.7208 (m-30) cc_final: 0.6707 (t70)
REVERT: A   90 THR cc_start: 0.7501 (m) cc_final: 0.7004 (m)
REVERT: A   94 ASN cc_start: 0.8169 (m-40) cc_final: 0.7579 (m110)
REVERT: A  138 TYR cc_start: 0.7969 (t80) cc_final: 0.7737 (t80)
REVERT: A  141 ARG cc_start: 0.8049 (mpp80) cc_final: 0.7791 (mpp80)
REVERT: A  146 ASP cc_start: 0.7385 (m-30) cc_final: 0.6928 (m-30)
REVERT: B  224 LEU cc_start: 0.7980 (tt) cc_final: 0.7763 (tt)
REVERT: B  291 LEU cc_start: 0.8617 (tp) cc_final: 0.8364 (tp)
REVERT: B  349 TYR cc_start: 0.7674 (m-10) cc_final: 0.7372 (m-10)
REVERT: B  366 LYS cc_start: 0.7263 (pptt) cc_final: 0.6756 (tmtt)
REVERT: B  430 TRP cc_start: 0.7066 (m100) cc_final: 0.6715 (m100)
REVERT: B  490 GLU cc_start: 0.8519 (tp30) cc_final: 0.8266 (tp30)
REVERT: B  523 PHE cc_start: 0.8381 (t80) cc_final: 0.8075 (t80)
REVERT: B  551 HIS cc_start: 0.8437 (t-90) cc_final: 0.7914 (t-90)
REVERT: B  734 LEU cc_start: 0.9205 (tt) cc_final: 0.8819 (tt)
REVERT: B  803 MET cc_start: 0.8323 (tmm) cc_final: 0.7709 (tmm)
REVERT: B  827 ASN cc_start: 0.8002 (t0) cc_final: 0.7721 (t0)
REVERT: C    7 ARG cc_start: 0.8236 (mmt-90) cc_final: 0.7989 (mmt180)
REVERT: C  134 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8208 (tp30)
REVERT: D   91 LYS cc_start: 0.8658 (tttp) cc_final: 0.8264 (mtmt)
REVERT: D   92 LYS cc_start: 0.8674 (mppt) cc_final: 0.7924 (tptt)
  outliers start: 2
  outliers final: 0
  residues processed: 238
  average time/residue: 0.0927
  time to fit residues: 30.1092
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  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 88 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   chunk 74 optimal weight:    6.9990
   chunk 67 optimal weight:    5.9990
   chunk 86 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
A 114 GLN
A 151 GLN
** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 196 GLN
B 327 ASN
B 478 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.137663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.110259 restraints weight = 20555.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.112870 restraints weight = 12827.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.114669 restraints weight = 9319.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.115810 restraints weight = 7553.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.116544 restraints weight = 6594.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.4837

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= 0.180
  Angle     :  0.774   8.870  12160  Z= 0.397
  Chirality :  0.050   0.249   1327
  Planarity :  0.004   0.039   1549
  Dihedral  :  9.374  58.140   1281
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  4.25 %
    Favored  : 95.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.89 (0.24), residues: 1065
  helix: -0.70 (0.19), residues: 654
  sheet: -1.69 (0.74), residues: 46
  loop : -2.04 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 134 
 TYR   0.025   0.002   TYR B 154 
 PHE   0.024   0.002   PHE B 716 
 TRP   0.026   0.002   TRP B 486 
 HIS   0.009   0.001   HIS B 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 9008)
  covalent geometry    : angle       0.77366 (12160)
  hydrogen bonds       : bond        0.04346 (  483)
  hydrogen bonds       : angle       4.84470 ( 1428)

*********************** 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: 2
    poor density    : 237
  time to evaluate  : 0.357 
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    7 GLU cc_start: 0.8397 (tp30) cc_final: 0.8097 (mm-30)
REVERT: A   53 ASP cc_start: 0.7325 (m-30) cc_final: 0.6775 (t70)
REVERT: A   94 ASN cc_start: 0.8207 (m-40) cc_final: 0.7220 (t0)
REVERT: A   98 ASN cc_start: 0.8646 (p0) cc_final: 0.8377 (p0)
REVERT: A  141 ARG cc_start: 0.8062 (mpp80) cc_final: 0.7807 (mpp80)
REVERT: A  146 ASP cc_start: 0.7402 (m-30) cc_final: 0.6968 (m-30)
REVERT: B  166 MET cc_start: 0.3881 (ppp) cc_final: 0.3473 (ppp)
REVERT: B  224 LEU cc_start: 0.8137 (tt) cc_final: 0.7893 (tt)
REVERT: B  291 LEU cc_start: 0.8725 (tp) cc_final: 0.8414 (tp)
REVERT: B  366 LYS cc_start: 0.7314 (pptt) cc_final: 0.6984 (tmtt)
REVERT: B  490 GLU cc_start: 0.8566 (tp30) cc_final: 0.8260 (tp30)
REVERT: B  523 PHE cc_start: 0.8366 (t80) cc_final: 0.8081 (t80)
REVERT: B  551 HIS cc_start: 0.8492 (t-90) cc_final: 0.8146 (t-90)
REVERT: B  710 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7537 (mp0)
REVERT: B  734 LEU cc_start: 0.9330 (tt) cc_final: 0.8817 (tt)
REVERT: B  738 MET cc_start: 0.8780 (mpp) cc_final: 0.8527 (mpp)
REVERT: B  803 MET cc_start: 0.8476 (tmm) cc_final: 0.7855 (tmm)
REVERT: B  827 ASN cc_start: 0.7984 (t0) cc_final: 0.7739 (t0)
REVERT: C    7 ARG cc_start: 0.8239 (mmt-90) cc_final: 0.7961 (mmt180)
REVERT: C  134 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8207 (tp30)
REVERT: C  137 TYR cc_start: 0.7786 (t80) cc_final: 0.7432 (t80)
REVERT: D   91 LYS cc_start: 0.8628 (tttp) cc_final: 0.8251 (mtmt)
REVERT: D   92 LYS cc_start: 0.8588 (mppt) cc_final: 0.7887 (tptt)
  outliers start: 2
  outliers final: 0
  residues processed: 238
  average time/residue: 0.0939
  time to fit residues: 31.1461
Evaluate side-chains
  180 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 62 optimal weight:    9.9990
   chunk 42 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 93 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 96 optimal weight:    7.9990
   chunk 101 optimal weight:   20.0000
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
A 148 HIS
B 159 HIS
B 478 ASN
C  71 HIS
D 116 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.139671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.112579 restraints weight = 20300.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.115240 restraints weight = 12393.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.117028 restraints weight = 8911.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.118232 restraints weight = 7174.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.118841 restraints weight = 6239.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.4969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9008  Z= 0.137
  Angle     :  0.734  11.599  12160  Z= 0.368
  Chirality :  0.047   0.231   1327
  Planarity :  0.004   0.044   1549
  Dihedral  :  9.002  57.758   1281
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.25), residues: 1065
  helix: -0.44 (0.20), residues: 654
  sheet: -1.86 (0.70), residues: 49
  loop : -1.87 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 137 
 TYR   0.023   0.001   TYR B 154 
 PHE   0.020   0.002   PHE B 515 
 TRP   0.021   0.002   TRP B 486 
 HIS   0.008   0.001   HIS B 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 9008)
  covalent geometry    : angle       0.73430 (12160)
  hydrogen bonds       : bond        0.03704 (  483)
  hydrogen bonds       : angle       4.61989 ( 1428)

*********************** 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: 0
    poor density    : 249
  time to evaluate  : 0.406 
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    7 GLU cc_start: 0.8420 (tp30) cc_final: 0.8087 (mm-30)
REVERT: A   53 ASP cc_start: 0.7227 (m-30) cc_final: 0.6896 (t70)
REVERT: A   90 THR cc_start: 0.7594 (m) cc_final: 0.7295 (m)
REVERT: A   94 ASN cc_start: 0.8151 (m-40) cc_final: 0.7667 (m110)
REVERT: A  110 TYR cc_start: 0.8515 (p90) cc_final: 0.7983 (p90)
REVERT: A  141 ARG cc_start: 0.8075 (mpp80) cc_final: 0.7803 (mpp80)
REVERT: A  146 ASP cc_start: 0.7406 (m-30) cc_final: 0.7018 (m-30)
REVERT: B  166 MET cc_start: 0.4041 (ppp) cc_final: 0.3549 (ppp)
REVERT: B  191 GLU cc_start: 0.7991 (tt0) cc_final: 0.7724 (tm-30)
REVERT: B  224 LEU cc_start: 0.8226 (tt) cc_final: 0.7962 (tt)
REVERT: B  291 LEU cc_start: 0.8661 (tp) cc_final: 0.8354 (tp)
REVERT: B  366 LYS cc_start: 0.7396 (pptt) cc_final: 0.6780 (tmtt)
REVERT: B  450 LYS cc_start: 0.7994 (ttpt) cc_final: 0.7665 (ttmm)
REVERT: B  490 GLU cc_start: 0.8533 (tp30) cc_final: 0.8227 (tp30)
REVERT: B  503 GLU cc_start: 0.5954 (pp20) cc_final: 0.5404 (pt0)
REVERT: B  523 PHE cc_start: 0.8306 (t80) cc_final: 0.7971 (t80)
REVERT: B  551 HIS cc_start: 0.8441 (t-90) cc_final: 0.8071 (t-90)
REVERT: B  710 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7614 (mp0)
REVERT: B  728 ASP cc_start: 0.7815 (p0) cc_final: 0.7056 (t0)
REVERT: B  734 LEU cc_start: 0.9354 (tt) cc_final: 0.8904 (tt)
REVERT: B  803 MET cc_start: 0.8306 (tmm) cc_final: 0.7666 (tmm)
REVERT: B  827 ASN cc_start: 0.8027 (t0) cc_final: 0.7775 (t0)
REVERT: C  134 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8198 (tp30)
REVERT: C  137 TYR cc_start: 0.7812 (t80) cc_final: 0.7420 (t80)
REVERT: D   91 LYS cc_start: 0.8610 (tttp) cc_final: 0.8229 (mtmt)
REVERT: D   92 LYS cc_start: 0.8709 (mppt) cc_final: 0.7964 (tptt)
REVERT: D  102 MET cc_start: 0.8669 (ppp) cc_final: 0.8361 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 249
  average time/residue: 0.0901
  time to fit residues: 31.0431
Evaluate side-chains
  190 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 64 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 16 optimal weight:    8.9990
   chunk 43 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 59 optimal weight:    0.6980
   chunk 61 optimal weight:    9.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.8580

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.140787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.113637 restraints weight = 20072.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.116322 restraints weight = 12280.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.118196 restraints weight = 8810.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.119316 restraints weight = 7065.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.120182 restraints weight = 6149.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.5089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9008  Z= 0.130
  Angle     :  0.728  11.684  12160  Z= 0.363
  Chirality :  0.047   0.236   1327
  Planarity :  0.004   0.041   1549
  Dihedral  :  8.762  58.419   1281
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.25), residues: 1065
  helix: -0.27 (0.20), residues: 655
  sheet: -1.88 (0.59), residues: 65
  loop : -1.75 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 137 
 TYR   0.023   0.001   TYR B 154 
 PHE   0.020   0.002   PHE B 716 
 TRP   0.019   0.002   TRP B 486 
 HIS   0.007   0.001   HIS B 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9008)
  covalent geometry    : angle       0.72783 (12160)
  hydrogen bonds       : bond        0.03598 (  483)
  hydrogen bonds       : angle       4.54689 ( 1428)

*********************** 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
  246 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 0.348 
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    7 GLU cc_start: 0.8408 (tp30) cc_final: 0.7999 (mm-30)
REVERT: A   90 THR cc_start: 0.7507 (m) cc_final: 0.7179 (m)
REVERT: A  141 ARG cc_start: 0.8128 (mpp80) cc_final: 0.7818 (mpp80)
REVERT: A  146 ASP cc_start: 0.7514 (m-30) cc_final: 0.7047 (m-30)
REVERT: B  173 GLU cc_start: 0.7896 (pp20) cc_final: 0.7693 (pp20)
REVERT: B  191 GLU cc_start: 0.8092 (tt0) cc_final: 0.7746 (tm-30)
REVERT: B  224 LEU cc_start: 0.8149 (tt) cc_final: 0.7896 (tt)
REVERT: B  291 LEU cc_start: 0.8656 (tp) cc_final: 0.8299 (tp)
REVERT: B  366 LYS cc_start: 0.7369 (pptt) cc_final: 0.6791 (tmtt)
REVERT: B  450 LYS cc_start: 0.8032 (ttpt) cc_final: 0.7591 (ttmm)
REVERT: B  490 GLU cc_start: 0.8505 (tp30) cc_final: 0.8218 (tp30)
REVERT: B  503 GLU cc_start: 0.5909 (pp20) cc_final: 0.5422 (pt0)
REVERT: B  523 PHE cc_start: 0.8270 (t80) cc_final: 0.8021 (t80)
REVERT: B  551 HIS cc_start: 0.8434 (t-90) cc_final: 0.8014 (t-90)
REVERT: B  710 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7621 (mp0)
REVERT: B  728 ASP cc_start: 0.7824 (p0) cc_final: 0.7054 (t0)
REVERT: B  734 LEU cc_start: 0.9310 (tt) cc_final: 0.8876 (tt)
REVERT: B  803 MET cc_start: 0.8297 (tmm) cc_final: 0.7663 (tmm)
REVERT: C   46 GLU cc_start: 0.7981 (pt0) cc_final: 0.7614 (pt0)
REVERT: C  134 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8200 (tp30)
REVERT: C  137 TYR cc_start: 0.7807 (t80) cc_final: 0.7431 (t80)
REVERT: D   91 LYS cc_start: 0.8576 (tttp) cc_final: 0.8266 (mtmt)
REVERT: D   92 LYS cc_start: 0.8747 (mppt) cc_final: 0.8117 (tptt)
REVERT: D  102 MET cc_start: 0.8722 (ppp) cc_final: 0.8490 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 246
  average time/residue: 0.0917
  time to fit residues: 31.0284
Evaluate side-chains
  186 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 102 optimal weight:    8.9990
   chunk 46 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 60 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 4 optimal weight:    6.9990
   chunk 66 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
A  95 HIS
** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 478 ASN
C  71 HIS
C 110 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.138319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.111679 restraints weight = 20317.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.114276 restraints weight = 12444.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.116069 restraints weight = 8972.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.117193 restraints weight = 7206.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.117831 restraints weight = 6279.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.5335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9008  Z= 0.159
  Angle     :  0.774  10.659  12160  Z= 0.389
  Chirality :  0.049   0.228   1327
  Planarity :  0.004   0.043   1549
  Dihedral  :  8.806  62.264   1281
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.25), residues: 1065
  helix: -0.23 (0.20), residues: 657
  sheet: -2.02 (0.59), residues: 65
  loop : -1.70 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  62 
 TYR   0.028   0.002   TYR B 158 
 PHE   0.023   0.002   PHE B 515 
 TRP   0.027   0.002   TRP B 486 
 HIS   0.007   0.001   HIS B 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 9008)
  covalent geometry    : angle       0.77422 (12160)
  hydrogen bonds       : bond        0.03980 (  483)
  hydrogen bonds       : angle       4.66610 ( 1428)

*********************** 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
  233 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.335 
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    7 GLU cc_start: 0.8462 (tp30) cc_final: 0.7933 (mm-30)
REVERT: A  141 ARG cc_start: 0.8162 (mpp80) cc_final: 0.7862 (mpp80)
REVERT: A  146 ASP cc_start: 0.7565 (m-30) cc_final: 0.7078 (m-30)
REVERT: B  291 LEU cc_start: 0.8592 (tp) cc_final: 0.8272 (tp)
REVERT: B  366 LYS cc_start: 0.7414 (pptt) cc_final: 0.6744 (tmtt)
REVERT: B  450 LYS cc_start: 0.8100 (ttpt) cc_final: 0.7634 (ttmm)
REVERT: B  490 GLU cc_start: 0.8542 (tp30) cc_final: 0.8274 (tp30)
REVERT: B  523 PHE cc_start: 0.8333 (t80) cc_final: 0.8053 (t80)
REVERT: B  551 HIS cc_start: 0.8465 (t-90) cc_final: 0.8130 (t-90)
REVERT: B  734 LEU cc_start: 0.9316 (tt) cc_final: 0.8861 (tt)
REVERT: B  738 MET cc_start: 0.8829 (mpp) cc_final: 0.8550 (mpp)
REVERT: B  803 MET cc_start: 0.8342 (tmm) cc_final: 0.7721 (tmm)
REVERT: C   46 GLU cc_start: 0.8055 (pt0) cc_final: 0.7810 (pt0)
REVERT: C  134 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8216 (tp30)
REVERT: C  137 TYR cc_start: 0.7882 (t80) cc_final: 0.7512 (t80)
REVERT: D   64 MET cc_start: 0.6664 (ppp) cc_final: 0.6392 (ppp)
REVERT: D   92 LYS cc_start: 0.8916 (mppt) cc_final: 0.8020 (tptt)
REVERT: D  102 MET cc_start: 0.8755 (ppp) cc_final: 0.8438 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 233
  average time/residue: 0.0937
  time to fit residues: 30.0549
Evaluate side-chains
  181 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 67 optimal weight:    5.9990
   chunk 100 optimal weight:   20.0000
   chunk 34 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 101 optimal weight:    7.9990
   chunk 36 optimal weight:    0.0270
   chunk 52 optimal weight:    0.7980
   chunk 103 optimal weight:    3.9990
   chunk 89 optimal weight:    6.9990
   overall best weight:    1.5242

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.139066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.111827 restraints weight = 20256.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.114507 restraints weight = 12276.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.116368 restraints weight = 8780.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.117643 restraints weight = 7025.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.118318 restraints weight = 6055.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.5483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9008  Z= 0.148
  Angle     :  0.764  11.325  12160  Z= 0.381
  Chirality :  0.048   0.221   1327
  Planarity :  0.004   0.040   1549
  Dihedral  :  8.648  62.833   1281
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.25), residues: 1065
  helix: -0.21 (0.20), residues: 654
  sheet: -2.11 (0.57), residues: 65
  loop : -1.62 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 137 
 TYR   0.031   0.002   TYR B 164 
 PHE   0.020   0.002   PHE B 716 
 TRP   0.029   0.002   TRP B 486 
 HIS   0.007   0.001   HIS B 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 9008)
  covalent geometry    : angle       0.76430 (12160)
  hydrogen bonds       : bond        0.03853 (  483)
  hydrogen bonds       : angle       4.64486 ( 1428)

*********************** 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
  236 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 GLU cc_start: 0.8481 (tp30) cc_final: 0.7972 (mm-30)
REVERT: A   94 ASN cc_start: 0.8090 (m110) cc_final: 0.7581 (m110)
REVERT: A  141 ARG cc_start: 0.8188 (mpp80) cc_final: 0.7885 (mpp80)
REVERT: A  146 ASP cc_start: 0.7562 (m-30) cc_final: 0.7040 (m-30)
REVERT: B  291 LEU cc_start: 0.8674 (tp) cc_final: 0.8306 (tp)
REVERT: B  366 LYS cc_start: 0.7256 (pptt) cc_final: 0.6758 (tmtt)
REVERT: B  450 LYS cc_start: 0.8060 (ttpt) cc_final: 0.7548 (ttmm)
REVERT: B  490 GLU cc_start: 0.8559 (tp30) cc_final: 0.8294 (tp30)
REVERT: B  523 PHE cc_start: 0.8300 (t80) cc_final: 0.7989 (t80)
REVERT: B  551 HIS cc_start: 0.8509 (t-90) cc_final: 0.8110 (t70)
REVERT: B  728 ASP cc_start: 0.7828 (p0) cc_final: 0.7114 (t0)
REVERT: B  734 LEU cc_start: 0.9269 (tt) cc_final: 0.8771 (tt)
REVERT: B  738 MET cc_start: 0.8851 (mpp) cc_final: 0.8577 (mpp)
REVERT: B  803 MET cc_start: 0.8321 (tmm) cc_final: 0.7696 (tmm)
REVERT: C   46 GLU cc_start: 0.8078 (pt0) cc_final: 0.7827 (pt0)
REVERT: C   91 MET cc_start: 0.8089 (tpp) cc_final: 0.7862 (tpp)
REVERT: C  134 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8238 (tp30)
REVERT: C  137 TYR cc_start: 0.7945 (t80) cc_final: 0.7555 (t80)
REVERT: D   64 MET cc_start: 0.6648 (ppp) cc_final: 0.6380 (ppp)
REVERT: D   91 LYS cc_start: 0.8608 (tttp) cc_final: 0.8217 (mtmt)
REVERT: D   92 LYS cc_start: 0.8757 (mppt) cc_final: 0.8073 (tptt)
REVERT: D  102 MET cc_start: 0.8714 (ppp) cc_final: 0.8471 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 236
  average time/residue: 0.0942
  time to fit residues: 30.6147
Evaluate side-chains
  184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9980
   chunk 27 optimal weight:    0.2980
   chunk 7 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 2 optimal weight:    0.8980
   chunk 66 optimal weight:    5.9990
   chunk 96 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 17 optimal weight:    8.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 478 ASN
C  71 HIS
D 116 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.141144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.114294 restraints weight = 19840.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.117104 restraints weight = 11998.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.119048 restraints weight = 8483.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.120336 restraints weight = 6745.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.121064 restraints weight = 5775.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
moved from start:          0.5580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9008  Z= 0.132
  Angle     :  0.757  12.269  12160  Z= 0.373
  Chirality :  0.047   0.216   1327
  Planarity :  0.004   0.040   1549
  Dihedral  :  8.363  61.461   1281
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.25), residues: 1065
  helix: -0.10 (0.20), residues: 661
  sheet: -2.10 (0.57), residues: 65
  loop : -1.60 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 137 
 TYR   0.033   0.002   TYR B 495 
 PHE   0.020   0.002   PHE C 102 
 TRP   0.022   0.002   TRP B 486 
 HIS   0.006   0.001   HIS B 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 9008)
  covalent geometry    : angle       0.75691 (12160)
  hydrogen bonds       : bond        0.03580 (  483)
  hydrogen bonds       : angle       4.61751 ( 1428)

********************** 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
  234 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 0.343 
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    7 GLU cc_start: 0.8421 (tp30) cc_final: 0.7866 (mm-30)
REVERT: A  141 ARG cc_start: 0.8175 (mpp80) cc_final: 0.7909 (mpp80)
REVERT: A  146 ASP cc_start: 0.7487 (m-30) cc_final: 0.6961 (m-30)
REVERT: B  173 GLU cc_start: 0.7674 (pp20) cc_final: 0.7431 (pp20)
REVERT: B  291 LEU cc_start: 0.8533 (tp) cc_final: 0.8142 (tp)
REVERT: B  366 LYS cc_start: 0.7267 (pptt) cc_final: 0.6775 (tmtt)
REVERT: B  450 LYS cc_start: 0.7783 (ttpt) cc_final: 0.7378 (ttmm)
REVERT: B  480 ASN cc_start: 0.8840 (t0) cc_final: 0.8621 (t0)
REVERT: B  490 GLU cc_start: 0.8474 (tp30) cc_final: 0.8202 (tp30)
REVERT: B  503 GLU cc_start: 0.5549 (pp20) cc_final: 0.5349 (pt0)
REVERT: B  523 PHE cc_start: 0.8219 (t80) cc_final: 0.7905 (t80)
REVERT: B  551 HIS cc_start: 0.8434 (t-90) cc_final: 0.8033 (t70)
REVERT: B  710 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7727 (mp0)
REVERT: B  728 ASP cc_start: 0.7673 (p0) cc_final: 0.6961 (t0)
REVERT: B  734 LEU cc_start: 0.9276 (tt) cc_final: 0.8786 (tt)
REVERT: B  738 MET cc_start: 0.8832 (mpp) cc_final: 0.8584 (mpp)
REVERT: B  803 MET cc_start: 0.8281 (tmm) cc_final: 0.7673 (tmm)
REVERT: C   46 GLU cc_start: 0.8049 (pt0) cc_final: 0.7799 (pt0)
REVERT: C   59 LYS cc_start: 0.8724 (tttp) cc_final: 0.8153 (tttp)
REVERT: C  134 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8196 (tp30)
REVERT: C  137 TYR cc_start: 0.7871 (t80) cc_final: 0.7504 (t80)
REVERT: D   64 MET cc_start: 0.6646 (ppp) cc_final: 0.6394 (ppp)
REVERT: D   91 LYS cc_start: 0.8465 (tttp) cc_final: 0.8193 (mtmt)
REVERT: D   92 LYS cc_start: 0.8748 (mppt) cc_final: 0.8179 (tptt)
REVERT: D  102 MET cc_start: 0.8634 (ppp) cc_final: 0.8372 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 234
  average time/residue: 0.0858
  time to fit residues: 27.8824
Evaluate side-chains
  184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 22 optimal weight:    0.4980
   chunk 98 optimal weight:    9.9990
   chunk 37 optimal weight:    0.7980
   chunk 1 optimal weight:    9.9990
   chunk 95 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 8 optimal weight:    0.1980
   chunk 39 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 124 GLN
B 159 HIS
B 178 GLN
B 478 ASN
D 116 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.141727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.115234 restraints weight = 19727.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.117958 restraints weight = 12149.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.119779 restraints weight = 8715.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.121024 restraints weight = 6983.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.121750 restraints weight = 6024.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.5648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9008  Z= 0.133
  Angle     :  0.758  12.619  12160  Z= 0.373
  Chirality :  0.047   0.211   1327
  Planarity :  0.004   0.040   1549
  Dihedral  :  8.044  60.659   1281
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.96 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.25), residues: 1065
  helix: -0.07 (0.20), residues: 664
  sheet: -2.01 (0.57), residues: 65
  loop : -1.62 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 137 
 TYR   0.029   0.002   TYR B 495 
 PHE   0.023   0.002   PHE B 515 
 TRP   0.020   0.002   TRP C  38 
 HIS   0.005   0.001   HIS B 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 9008)
  covalent geometry    : angle       0.75814 (12160)
  hydrogen bonds       : bond        0.03618 (  483)
  hydrogen bonds       : angle       4.54295 ( 1428)

===============================================================================
Job complete
usr+sys time: 1533.51 seconds
wall clock time: 27 minutes 10.20 seconds (1630.20 seconds total)