Starting phenix.real_space_refine
on Sun Aug 24 02:17:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hak_34594/08_2025/8hak_34594.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hak_34594/08_2025/8hak_34594.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hak_34594/08_2025/8hak_34594.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hak_34594/08_2025/8hak_34594.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hak_34594/08_2025/8hak_34594.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hak_34594/08_2025/8hak_34594.cif"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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     292      5.49       5
     S      47      5.16       5
     C    9421      2.51       5
     N    2979      2.21       5
     O    3603      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 119 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16342
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 794
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 648
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "C"
      Number of atoms: 806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 806
          Classifications: {'peptide': 105}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 717
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 717
          Classifications: {'peptide': 91}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 89}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ALY:plan-2': 2, 'ALY:plan-1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "G"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 815
          Classifications: {'peptide': 106}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "H"
      Number of atoms: 741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 741
          Classifications: {'peptide': 95}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "J"
      Number of atoms: 3016
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3016
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 2973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2973
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "N"
      Number of atoms: 4295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 520, 4295
          Classifications: {'peptide': 520}
          Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 487}
          Chain breaks: 3
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   ALA C  14 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA C  14 " occ=0.00
  Time building chain proxies: 3.56, per 1000 atoms: 0.22
  Number of scatterers: 16342
  At special positions: 0
  Unit cell: (123.48, 124.95, 152.88, 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      47     16.00
     P     292     15.00
     O    3603      8.00
     N    2979      7.00
     C    9421      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.15
  Conformation dependent library (CDL) restraints added in 398.5 milliseconds
  
  Enol-peptide restraints added in 1.7 microseconds
  

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2422

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 13 sheets defined
      61.8% alpha, 7.0% beta
      101 base pairs and 219 stacking pairs defined.
    Time for finding SS restraints: 2.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 56
    Processing helix  chain 'A' and resid 63 through 77
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.702A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.522A  pdb=" N   GLY B  28 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.787A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 3.947A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.600A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.511A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.881A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 122
      removed outlier: 4.119A  pdb=" N   SER D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.538A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.782A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 83 through 93
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.342A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.818A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
    Processing helix  chain 'N' and resid 1052 through 1068
      Proline residue:  N1060  - end of helix
      removed outlier: 3.523A  pdb=" N   GLN N1068 " --> pdb=" O   ALA N1064 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 1072 through 1076
    Processing helix  chain 'N' and resid 1080 through 1085
    Processing helix  chain 'N' and resid 1098 through 1109
      removed outlier: 3.610A  pdb=" N   ILE N1102 " --> pdb=" O   ASP N1098 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 1113 through 1131
      removed outlier: 3.958A  pdb=" N   TYR N1117 " --> pdb=" O   GLU N1113 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 1136 through 1160
      removed outlier: 3.728A  pdb=" N   LYS N1140 " --> pdb=" O   SER N1136 " (cutoff:3.500A)
      Proline residue:  N1155  - end of helix
    Processing helix  chain 'N' and resid 1256 through 1260
    Processing helix  chain 'N' and resid 1272 through 1280
    Processing helix  chain 'N' and resid 1289 through 1293
    Processing helix  chain 'N' and resid 1296 through 1314
    Processing helix  chain 'N' and resid 1336 through 1343
      removed outlier: 3.818A  pdb=" N   ARG N1342 " --> pdb=" O   GLY N1338 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 1406 through 1429
      removed outlier: 4.391A  pdb=" N   THR N1411 " --> pdb=" O   LYS N1407 " (cutoff:3.500A)
      removed outlier: 4.893A  pdb=" N   ALA N1412 " --> pdb=" O   CYS N1408 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   LEU N1422 " --> pdb=" O   LEU N1418 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 1459 through 1477
    Processing helix  chain 'N' and resid 1486 through 1494
    Processing helix  chain 'N' and resid 1497 through 1501
    Processing helix  chain 'N' and resid 1507 through 1519
      removed outlier: 3.893A  pdb=" N   ASN N1511 " --> pdb=" O   ASP N1507 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   GLU N1514 " --> pdb=" O   PRO N1510 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 1580 through 1591
    Processing helix  chain 'N' and resid 1626 through 1638
      removed outlier: 4.070A  pdb=" N   PHE N1630 " --> pdb=" O   GLY N1626 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 1643 through 1662
      removed outlier: 3.591A  pdb=" N   SER N1662 " --> pdb=" O   LEU N1658 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.870A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.536A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97
      removed outlier: 6.229A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.535A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 101
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.844A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.091A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'N' and resid 1198 through 1200
    Processing sheet with id=AB3, first strand: chain 'N' and resid 1244 through 1246
    Processing sheet with id=AB4, first strand: chain 'N' and resid 1321 through 1334
      removed outlier: 6.510A  pdb=" N   ALA N1359 " --> pdb=" O   VAL N1326 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   ALA N1328 " --> pdb=" O   THR N1357 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   THR N1357 " --> pdb=" O   ALA N1328 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   ASP N1330 " --> pdb=" O   TYR N1355 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   TYR N1355 " --> pdb=" O   ASP N1330 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   THR N1332 " --> pdb=" O   PHE N1353 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   PHE N1353 " --> pdb=" O   THR N1332 " (cutoff:3.500A)
      removed outlier: 5.283A  pdb=" N   TYR N1381 " --> pdb=" O   PRO N1354 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   ARG N1356 " --> pdb=" O   GLN N1379 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   GLN N1379 " --> pdb=" O   ARG N1356 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   LYS N1358 " --> pdb=" O   HIS N1377 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   HIS N1377 " --> pdb=" O   LYS N1358 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   LEU N1360 " --> pdb=" O   GLY N1375 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   GLY N1375 " --> pdb=" O   LEU N1360 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   ALA N1362 " --> pdb=" O   PHE N1373 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   TYR N1397 " --> pdb=" O   HIS N1377 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   GLN N1379 " --> pdb=" O   ILE N1395 " (cutoff:3.500A)
      removed outlier: 5.584A  pdb=" N   ILE N1395 " --> pdb=" O   GLN N1379 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   TYR N1381 " --> pdb=" O   VAL N1393 " (cutoff:3.500A)
      removed outlier: 5.414A  pdb=" N   VAL N1393 " --> pdb=" O   TYR N1381 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   TRP N1436 " --> pdb=" O   ILE N1395 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   TYR N1397 " --> pdb=" O   TRP N1436 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ASP N1482 " --> pdb=" O   ARG N1599 " (cutoff:3.500A)

    588 hydrogen bonds defined for protein.
    1728 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      243 hydrogen bonds
      486 hydrogen bond angles
      0 basepair planarities
      101 basepair parallelities
      219 stacking parallelities
  Total time for adding SS restraints: 2.95

  Time building geometry restraints manager: 1.50 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3703
        1.34 -     1.46: 4900
        1.46 -     1.57: 8011
        1.57 -     1.69: 582
        1.69 -     1.81: 70
  Bond restraints: 17266
  Sorted by residual:
  bond pdb=" CG  GLU F  74 "
       pdb=" CD  GLU F  74 "
    ideal  model  delta    sigma   weight residual
    1.516  1.457  0.059 2.50e-02 1.60e+03 5.55e+00
  bond pdb=" CG  GLU H 113 "
       pdb=" CD  GLU H 113 "
    ideal  model  delta    sigma   weight residual
    1.516  1.462  0.054 2.50e-02 1.60e+03 4.74e+00
  bond pdb=" NZ  ALY F  12 "
       pdb=" CH  ALY F  12 "
    ideal  model  delta    sigma   weight residual
    1.343  1.384 -0.041 2.00e-02 2.50e+03 4.22e+00
  bond pdb=" CG  GLU B  74 "
       pdb=" CD  GLU B  74 "
    ideal  model  delta    sigma   weight residual
    1.516  1.477  0.039 2.50e-02 1.60e+03 2.49e+00
  bond pdb=" CG  GLU B  63 "
       pdb=" CD  GLU B  63 "
    ideal  model  delta    sigma   weight residual
    1.516  1.479  0.037 2.50e-02 1.60e+03 2.17e+00
  ... (remaining 17261 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 23911
        1.81 -     3.63: 596
        3.63 -     5.44: 46
        5.44 -     7.26: 16
        7.26 -     9.07: 3
  Bond angle restraints: 24572
  Sorted by residual:
  angle pdb=" N   GLU F  74 "
        pdb=" CA  GLU F  74 "
        pdb=" CB  GLU F  74 "
      ideal   model   delta    sigma   weight residual
     110.30  117.95   -7.65 1.54e+00 4.22e-01 2.47e+01
  angle pdb=" N   GLU B  63 "
        pdb=" CA  GLU B  63 "
        pdb=" CB  GLU B  63 "
      ideal   model   delta    sigma   weight residual
     110.28  117.64   -7.36 1.55e+00 4.16e-01 2.26e+01
  angle pdb=" N   GLU H 113 "
        pdb=" CA  GLU H 113 "
        pdb=" CB  GLU H 113 "
      ideal   model   delta    sigma   weight residual
     110.28  116.50   -6.22 1.55e+00 4.16e-01 1.61e+01
  angle pdb=" N   GLU C  56 "
        pdb=" CA  GLU C  56 "
        pdb=" CB  GLU C  56 "
      ideal   model   delta    sigma   weight residual
     110.22  116.15   -5.93 1.54e+00 4.22e-01 1.49e+01
  angle pdb=" N   GLU B  74 "
        pdb=" CA  GLU B  74 "
        pdb=" CB  GLU B  74 "
      ideal   model   delta    sigma   weight residual
     110.39  116.42   -6.03 1.66e+00 3.63e-01 1.32e+01
  ... (remaining 24567 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.08: 8349
       34.08 -    68.16: 1354
       68.16 -   102.24: 34
      102.24 -   136.32: 0
      136.32 -   170.40: 2
  Dihedral angle restraints: 9739
    sinusoidal: 5988
      harmonic: 3751
  Sorted by residual:
  dihedral pdb=" C4'  DT K 136 "
           pdb=" C3'  DT K 136 "
           pdb=" O3'  DT K 136 "
           pdb=" P    DT K 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   30.40 -170.40     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DA J  59 "
           pdb=" C3'  DA J  59 "
           pdb=" O3'  DA J  59 "
           pdb=" P    DA J  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   51.81  168.19     1      3.50e+01 8.16e-04 1.55e+01
  dihedral pdb=" CG  ARG E 128 "
           pdb=" CD  ARG E 128 "
           pdb=" NE  ARG E 128 "
           pdb=" CZ  ARG E 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -134.23   44.23     2      1.50e+01 4.44e-03 1.04e+01
  ... (remaining 9736 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 2099
       0.037 -    0.074: 486
       0.074 -    0.111: 125
       0.111 -    0.148: 26
       0.148 -    0.185: 2
  Chirality restraints: 2738
  Sorted by residual:
  chirality pdb=" CG  LEU C  55 "
            pdb=" CB  LEU C  55 "
            pdb=" CD1 LEU C  55 "
            pdb=" CD2 LEU C  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 8.57e-01
  chirality pdb=" CA  ASP B  24 "
            pdb=" N   ASP B  24 "
            pdb=" C   ASP B  24 "
            pdb=" CB  ASP B  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.88e-01
  chirality pdb=" CA  GLU G  61 "
            pdb=" N   GLU G  61 "
            pdb=" C   GLU G  61 "
            pdb=" CB  GLU G  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.43e-01
  ... (remaining 2735 not shown)

  Planarity restraints: 2114
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E  67 "   -0.014 2.00e-02 2.50e+03   2.18e-02 8.35e+00
        pdb=" CG  PHE E  67 "    0.047 2.00e-02 2.50e+03
        pdb=" CD1 PHE E  67 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE E  67 "   -0.027 2.00e-02 2.50e+03
        pdb=" CE1 PHE E  67 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE E  67 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  PHE E  67 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP N1069 "   -0.038 5.00e-02 4.00e+02   5.77e-02 5.32e+00
        pdb=" N   PRO N1070 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO N1070 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO N1070 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU H 113 "    0.010 2.00e-02 2.50e+03   2.04e-02 4.17e+00
        pdb=" CD  GLU H 113 "   -0.035 2.00e-02 2.50e+03
        pdb=" OE1 GLU H 113 "    0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU H 113 "    0.013 2.00e-02 2.50e+03
  ... (remaining 2111 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1764
        2.75 -     3.29: 16104
        3.29 -     3.83: 31878
        3.83 -     4.36: 36857
        4.36 -     4.90: 53627
  Nonbonded interactions: 140230
  Sorted by model distance:
  nonbonded pdb=" OG  SER C  18 "
            pdb=" O   LEU C  23 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" O   GLU B  74 "
            pdb=" NH2 ARG D  92 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" N   THR H  90 "
            pdb=" OE2 GLU H  93 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" O   VAL N1156 "
            pdb=" OG  SER N1159 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" NH1 ARG G  29 "
            pdb=" O   SER H  36 "
     model   vdw
     2.287 3.120
  ... (remaining 140225 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'E' and resid 39 through 134)
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 21 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and (resid 14 through 117 or (resid 118 and (name N or name CA or nam \ 
e C or name O or name CB ))))
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and resid 31 through 124)
}
ncs_group {
  reference = (chain 'J' and resid 19 through 162)
  selection = (chain 'K' and resid 19 through 162)
}

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=0.00 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:             1.470
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     15.430
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  17266  Z= 0.162
  Angle     :  0.652   9.072  24572  Z= 0.397
  Chirality :  0.036   0.185   2738
  Planarity :  0.004   0.058   2114
  Dihedral  : 24.736 170.401   7317
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.22), residues: 1256
  helix:  0.91 (0.18), residues: 744
  sheet:  0.55 (0.73), residues: 54
  loop : -0.44 (0.26), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  99 
 TYR   0.022   0.001   TYR C  50 
 PHE   0.047   0.002   PHE E  67 
 TRP   0.033   0.002   TRP N1129 
 HIS   0.005   0.001   HIS D 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (17266)
  covalent geometry    : angle       0.65223 (24572)
  hydrogen bonds       : bond        0.12636 (  831)
  hydrogen bonds       : angle       5.52509 ( 2214)

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8492 (mt-10)
REVERT: A  106 ASP cc_start: 0.8794 (m-30) cc_final: 0.8572 (m-30)
REVERT: B   63 GLU cc_start: 0.9155 (pm20) cc_final: 0.8665 (pm20)
REVERT: D   68 ASP cc_start: 0.9087 (m-30) cc_final: 0.8875 (m-30)
REVERT: D   95 GLN cc_start: 0.9339 (mt0) cc_final: 0.9049 (mp10)
REVERT: D  108 LYS cc_start: 0.9620 (mtpp) cc_final: 0.9390 (mmmt)
REVERT: E   77 ASP cc_start: 0.8590 (m-30) cc_final: 0.8219 (t0)
REVERT: E   90 MET cc_start: 0.9021 (mmp) cc_final: 0.8524 (mmp)
REVERT: E  120 MET cc_start: 0.8273 (tpt) cc_final: 0.8053 (mmm)
REVERT: F   62 LEU cc_start: 0.9690 (mt) cc_final: 0.9389 (mt)
REVERT: F   93 GLN cc_start: 0.8752 (tt0) cc_final: 0.8184 (tm-30)
REVERT: G   24 GLN cc_start: 0.8919 (mp10) cc_final: 0.8692 (mp10)
REVERT: G   38 ASN cc_start: 0.8572 (m-40) cc_final: 0.8264 (p0)
REVERT: G   51 LEU cc_start: 0.9515 (tp) cc_final: 0.9256 (tp)
REVERT: G   68 ASN cc_start: 0.8798 (m-40) cc_final: 0.8256 (t0)
REVERT: G   72 ASP cc_start: 0.9130 (m-30) cc_final: 0.8781 (m-30)
REVERT: H   41 VAL cc_start: 0.9328 (t) cc_final: 0.9099 (t)
REVERT: N 1349 MET cc_start: -0.2944 (tpt) cc_final: -0.3440 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.1022
  time to fit residues: 28.6397
Evaluate side-chains
  123 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:   20.0000
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    4.9990
   chunk 149 optimal weight:   30.0000
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N1236 ASN
N1379 GLN
N1415 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.067587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.045767 restraints weight = 154379.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.047042 restraints weight = 79359.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.047816 restraints weight = 52731.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.048115 restraints weight = 41692.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.048197 restraints weight = 37330.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.112  17266  Z= 0.242
  Angle     :  0.633   9.276  24572  Z= 0.368
  Chirality :  0.038   0.179   2738
  Planarity :  0.005   0.066   2114
  Dihedral  : 28.633 174.681   4715
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.34 %
    Favored  : 96.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.22), residues: 1256
  helix:  1.40 (0.18), residues: 762
  sheet:  0.51 (0.73), residues: 55
  loop : -0.40 (0.27), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  79 
 TYR   0.015   0.001   TYR F  98 
 PHE   0.027   0.002   PHE N1149 
 TRP   0.014   0.003   TRP N1122 
 HIS   0.006   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 (17266)
  covalent geometry    : angle       0.63336 (24572)
  hydrogen bonds       : bond        0.06587 (  831)
  hydrogen bonds       : angle       3.92167 ( 2214)

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 163
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 PHE cc_start: 0.8728 (m-10) cc_final: 0.8408 (m-10)
REVERT: A   97 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8646 (mt-10)
REVERT: B   63 GLU cc_start: 0.9246 (OUTLIER) cc_final: 0.9040 (pp20)
REVERT: B   97 LEU cc_start: 0.9093 (tp) cc_final: 0.8879 (tp)
REVERT: C   38 ASN cc_start: 0.8315 (t0) cc_final: 0.7513 (t0)
REVERT: C  112 GLN cc_start: 0.8805 (mp10) cc_final: 0.8592 (mp10)
REVERT: D   68 ASP cc_start: 0.9093 (m-30) cc_final: 0.8872 (m-30)
REVERT: D   86 ARG cc_start: 0.8913 (mmp80) cc_final: 0.8651 (mmp80)
REVERT: D   95 GLN cc_start: 0.9398 (mt0) cc_final: 0.9186 (mt0)
REVERT: D  121 TYR cc_start: 0.8137 (t80) cc_final: 0.7891 (t80)
REVERT: E   97 GLU cc_start: 0.9430 (mt-10) cc_final: 0.8652 (mm-30)
REVERT: E  120 MET cc_start: 0.8683 (tpt) cc_final: 0.8458 (mmm)
REVERT: F   93 GLN cc_start: 0.8837 (tt0) cc_final: 0.8303 (tm-30)
REVERT: G   38 ASN cc_start: 0.8910 (m-40) cc_final: 0.8025 (t0)
REVERT: G   64 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8784 (mm-30)
REVERT: G   68 ASN cc_start: 0.8966 (m-40) cc_final: 0.8567 (t0)
REVERT: G   72 ASP cc_start: 0.9151 (m-30) cc_final: 0.8600 (m-30)
REVERT: G   74 LYS cc_start: 0.9408 (mmmm) cc_final: 0.9174 (tptp)
REVERT: H   83 TYR cc_start: 0.8858 (m-10) cc_final: 0.8578 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 163
  average time/residue: 0.1089
  time to fit residues: 26.8291
Evaluate side-chains
  118 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 128 optimal weight:    0.4980
   chunk 94 optimal weight:    5.9990
   chunk 146 optimal weight:    6.9990
   chunk 106 optimal weight:    5.9990
   chunk 71 optimal weight:    0.0010
   chunk 40 optimal weight:    0.8980
   chunk 129 optimal weight:    8.9990
   chunk 14 optimal weight:    5.9990
   chunk 80 optimal weight:    5.9990
   chunk 82 optimal weight:    6.9990
   overall best weight:    2.6790

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

Flipped N/Q/H residues before XYZ refinement:
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N1236 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.065002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.043182 restraints weight = 156382.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.044445 restraints weight = 79871.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.045236 restraints weight = 53038.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.045566 restraints weight = 42042.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.045701 restraints weight = 37675.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  17266  Z= 0.202
  Angle     :  0.601   8.106  24572  Z= 0.351
  Chirality :  0.036   0.152   2738
  Planarity :  0.005   0.083   2114
  Dihedral  : 29.140 177.872   4715
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.70 %
    Favored  : 96.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.23), residues: 1256
  helix:  1.55 (0.18), residues: 760
  sheet:  0.41 (0.69), residues: 60
  loop : -0.27 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  79 
 TYR   0.016   0.002   TYR G  57 
 PHE   0.018   0.002   PHE N1595 
 TRP   0.024   0.003   TRP N1509 
 HIS   0.004   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 (17266)
  covalent geometry    : angle       0.60069 (24572)
  hydrogen bonds       : bond        0.05268 (  831)
  hydrogen bonds       : angle       3.72735 ( 2214)

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 163
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9126 (tt0) cc_final: 0.8739 (tt0)
REVERT: A   97 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8602 (mt-10)
REVERT: A  120 MET cc_start: 0.8005 (mpp) cc_final: 0.7802 (mpp)
REVERT: B   74 GLU cc_start: 0.9218 (pp20) cc_final: 0.8828 (pp20)
REVERT: B   84 MET cc_start: 0.8642 (tpt) cc_final: 0.8347 (tpp)
REVERT: C   38 ASN cc_start: 0.8404 (t0) cc_final: 0.7261 (t0)
REVERT: C   56 GLU cc_start: 0.8680 (mp0) cc_final: 0.8436 (mp0)
REVERT: C  112 GLN cc_start: 0.8760 (mp10) cc_final: 0.8496 (mp10)
REVERT: D   62 MET cc_start: 0.9585 (mmm) cc_final: 0.9337 (mmm)
REVERT: D   65 PHE cc_start: 0.9762 (t80) cc_final: 0.9323 (t80)
REVERT: D   68 ASP cc_start: 0.8998 (m-30) cc_final: 0.8658 (m-30)
REVERT: D   86 ARG cc_start: 0.8968 (mmp80) cc_final: 0.8639 (mmp80)
REVERT: D   95 GLN cc_start: 0.9418 (mt0) cc_final: 0.8964 (mp10)
REVERT: E   90 MET cc_start: 0.9104 (mmp) cc_final: 0.8902 (mmm)
REVERT: E   97 GLU cc_start: 0.9468 (mt-10) cc_final: 0.8845 (mm-30)
REVERT: E  110 CYS cc_start: 0.9715 (m) cc_final: 0.9026 (t)
REVERT: E  120 MET cc_start: 0.8970 (tpt) cc_final: 0.8680 (mmm)
REVERT: F   62 LEU cc_start: 0.9722 (mt) cc_final: 0.9505 (mp)
REVERT: F   88 TYR cc_start: 0.8617 (m-10) cc_final: 0.7918 (m-10)
REVERT: F   93 GLN cc_start: 0.8813 (tt0) cc_final: 0.8434 (tm-30)
REVERT: G   38 ASN cc_start: 0.8978 (m-40) cc_final: 0.8131 (t0)
REVERT: G   39 TYR cc_start: 0.8972 (m-80) cc_final: 0.8763 (m-80)
REVERT: G   74 LYS cc_start: 0.9442 (mmmm) cc_final: 0.9184 (tptp)
REVERT: G   99 ARG cc_start: 0.7783 (tpt90) cc_final: 0.7453 (mmm160)
REVERT: G  100 VAL cc_start: 0.8849 (t) cc_final: 0.8640 (t)
REVERT: N 1349 MET cc_start: 0.2726 (tpt) cc_final: 0.1956 (tpt)
REVERT: N 1624 MET cc_start: -0.1333 (mmm) cc_final: -0.1651 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 164
  average time/residue: 0.1120
  time to fit residues: 27.6978
Evaluate side-chains
  114 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 113 optimal weight:   30.0000
   chunk 73 optimal weight:   20.0000
   chunk 66 optimal weight:    0.2980
   chunk 59 optimal weight:    2.9990
   chunk 149 optimal weight:   20.0000
   chunk 22 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 152 optimal weight:    7.9990
   chunk 109 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
E  68 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N1236 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.065300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.043076 restraints weight = 152897.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.044289 restraints weight = 77176.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 70)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.045044 restraints weight = 50774.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.045401 restraints weight = 40137.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.045668 restraints weight = 35957.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.3259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  17266  Z= 0.150
  Angle     :  0.562   8.008  24572  Z= 0.327
  Chirality :  0.035   0.142   2738
  Planarity :  0.004   0.066   2114
  Dihedral  : 29.136 178.429   4715
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.89 %
    Favored  : 98.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.23), residues: 1256
  helix:  1.69 (0.18), residues: 761
  sheet:  0.27 (0.73), residues: 55
  loop : -0.25 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  29 
 TYR   0.012   0.001   TYR F  98 
 PHE   0.017   0.001   PHE E  67 
 TRP   0.010   0.001   TRP N1115 
 HIS   0.004   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (17266)
  covalent geometry    : angle       0.56172 (24572)
  hydrogen bonds       : bond        0.04328 (  831)
  hydrogen bonds       : angle       3.48629 ( 2214)

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 171
  time to evaluate  : 0.313 
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   84 PHE cc_start: 0.8477 (m-10) cc_final: 0.8118 (m-10)
REVERT: A   94 GLU cc_start: 0.9048 (tt0) cc_final: 0.8633 (tt0)
REVERT: A   97 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8540 (mt-10)
REVERT: B   74 GLU cc_start: 0.9253 (pp20) cc_final: 0.8907 (pp20)
REVERT: B   84 MET cc_start: 0.8588 (tpt) cc_final: 0.8337 (tpp)
REVERT: D   65 PHE cc_start: 0.9769 (t80) cc_final: 0.9450 (t80)
REVERT: D   68 ASP cc_start: 0.9080 (m-30) cc_final: 0.8709 (m-30)
REVERT: D   86 ARG cc_start: 0.8879 (mmp80) cc_final: 0.8524 (mmp80)
REVERT: D   95 GLN cc_start: 0.9424 (mt0) cc_final: 0.9220 (mt0)
REVERT: E   90 MET cc_start: 0.9008 (mmp) cc_final: 0.8706 (mmm)
REVERT: E   97 GLU cc_start: 0.9472 (mt-10) cc_final: 0.8760 (mm-30)
REVERT: F   59 LYS cc_start: 0.9015 (ptpp) cc_final: 0.8764 (ptpp)
REVERT: F   62 LEU cc_start: 0.9740 (mt) cc_final: 0.9526 (mt)
REVERT: F   63 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8487 (mp0)
REVERT: F   88 TYR cc_start: 0.8538 (m-10) cc_final: 0.7764 (m-10)
REVERT: F   93 GLN cc_start: 0.8825 (tt0) cc_final: 0.8354 (tm-30)
REVERT: G   38 ASN cc_start: 0.8966 (m-40) cc_final: 0.8687 (p0)
REVERT: G   39 TYR cc_start: 0.9093 (m-80) cc_final: 0.8782 (m-80)
REVERT: G   74 LYS cc_start: 0.9442 (mmmm) cc_final: 0.9206 (mmmm)
REVERT: G   99 ARG cc_start: 0.7843 (tpt90) cc_final: 0.7425 (mmm160)
  outliers start: 1
  outliers final: 0
  residues processed: 172
  average time/residue: 0.1106
  time to fit residues: 28.3457
Evaluate side-chains
  116 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 150 optimal weight:   20.0000
   chunk 112 optimal weight:   30.0000
   chunk 133 optimal weight:    5.9990
   chunk 15 optimal weight:    6.9990
   chunk 126 optimal weight:    7.9990
   chunk 132 optimal weight:   50.0000
   chunk 10 optimal weight:    1.9990
   chunk 62 optimal weight:    9.9990
   chunk 9 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
C  68 ASN
C 104 GLN
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
G  31 HIS
G 110 ASN
** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N1236 ASN
N1261 HIS
** N1451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N1591 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.055189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.033744 restraints weight = 146525.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.034664 restraints weight = 79430.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.035225 restraints weight = 55069.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.035497 restraints weight = 44739.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.035705 restraints weight = 40298.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.4986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.099  17266  Z= 0.354
  Angle     :  0.742   9.523  24572  Z= 0.425
  Chirality :  0.043   0.270   2738
  Planarity :  0.006   0.072   2114
  Dihedral  : 29.957 177.534   4715
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 19.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.52 %
    Favored  : 96.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.22), residues: 1256
  helix:  1.18 (0.17), residues: 765
  sheet: -0.12 (0.68), residues: 55
  loop : -0.35 (0.27), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG N1392 
 TYR   0.024   0.002   TYR G  57 
 PHE   0.032   0.002   PHE N1508 
 TRP   0.023   0.003   TRP N1436 
 HIS   0.005   0.002   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00773 (17266)
  covalent geometry    : angle       0.74190 (24572)
  hydrogen bonds       : bond        0.09785 (  831)
  hydrogen bonds       : angle       4.30775 ( 2214)

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9549 (mm-30) cc_final: 0.9156 (mm-30)
REVERT: A   94 GLU cc_start: 0.9125 (tt0) cc_final: 0.8646 (tt0)
REVERT: A   97 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8316 (mp0)
REVERT: A  106 ASP cc_start: 0.9253 (m-30) cc_final: 0.8821 (m-30)
REVERT: B   63 GLU cc_start: 0.9261 (pm20) cc_final: 0.9027 (pm20)
REVERT: B   74 GLU cc_start: 0.9365 (pp20) cc_final: 0.8991 (pp20)
REVERT: B   84 MET cc_start: 0.8700 (tpt) cc_final: 0.8388 (tpp)
REVERT: D   68 ASP cc_start: 0.9196 (m-30) cc_final: 0.8841 (m-30)
REVERT: D   86 ARG cc_start: 0.9116 (mmp80) cc_final: 0.8646 (mmp80)
REVERT: D  121 TYR cc_start: 0.9106 (t80) cc_final: 0.8886 (t80)
REVERT: E   90 MET cc_start: 0.9072 (mmp) cc_final: 0.8828 (mmm)
REVERT: E   97 GLU cc_start: 0.9413 (mt-10) cc_final: 0.8876 (mm-30)
REVERT: E  110 CYS cc_start: 0.9713 (m) cc_final: 0.9186 (t)
REVERT: F   84 MET cc_start: 0.8902 (tpp) cc_final: 0.8610 (tpp)
REVERT: F   87 VAL cc_start: 0.9500 (t) cc_final: 0.9252 (t)
REVERT: F   88 TYR cc_start: 0.8632 (m-10) cc_final: 0.7851 (m-10)
REVERT: F   93 GLN cc_start: 0.8857 (tt0) cc_final: 0.8625 (tm-30)
REVERT: G   38 ASN cc_start: 0.9136 (m-40) cc_final: 0.8760 (p0)
REVERT: G   39 TYR cc_start: 0.9250 (m-80) cc_final: 0.8885 (m-80)
REVERT: G   64 GLU cc_start: 0.9290 (mm-30) cc_final: 0.9086 (mm-30)
REVERT: G   74 LYS cc_start: 0.9458 (mmmm) cc_final: 0.9254 (mmmm)
REVERT: H   37 TYR cc_start: 0.9101 (m-80) cc_final: 0.8848 (m-10)
REVERT: H   41 VAL cc_start: 0.9550 (t) cc_final: 0.9341 (t)
REVERT: N 1349 MET cc_start: 0.4034 (tpt) cc_final: 0.3506 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1151
  time to fit residues: 24.5304
Evaluate side-chains
  93 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 112 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 10 optimal weight:    0.6980
   chunk 136 optimal weight:   20.0000
   chunk 73 optimal weight:   20.0000
   chunk 17 optimal weight:    6.9990
   chunk 145 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 123 optimal weight:   20.0000
   overall best weight:    2.6984

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

Flipped N/Q/H residues before XYZ refinement:
E  55 GLN
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.060861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.038925 restraints weight = 156825.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.039919 restraints weight = 80739.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.040631 restraints weight = 53879.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.040899 restraints weight = 42842.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.041084 restraints weight = 38473.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.5103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  17266  Z= 0.203
  Angle     :  0.630  10.346  24572  Z= 0.362
  Chirality :  0.037   0.171   2738
  Planarity :  0.005   0.071   2114
  Dihedral  : 30.078 178.892   4715
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.89 %
    Favored  : 97.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.22), residues: 1256
  helix:  1.45 (0.18), residues: 762
  sheet: -0.01 (0.70), residues: 55
  loop : -0.29 (0.27), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  99 
 TYR   0.024   0.002   TYR N1394 
 PHE   0.011   0.001   PHE E  67 
 TRP   0.016   0.002   TRP N1115 
 HIS   0.006   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 (17266)
  covalent geometry    : angle       0.62990 (24572)
  hydrogen bonds       : bond        0.05286 (  831)
  hydrogen bonds       : angle       3.87541 ( 2214)

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 145
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9551 (mm-30) cc_final: 0.9204 (mm-30)
REVERT: A   94 GLU cc_start: 0.9016 (tt0) cc_final: 0.8609 (tt0)
REVERT: A   97 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8202 (mp0)
REVERT: A  110 CYS cc_start: 0.8800 (t) cc_final: 0.8489 (t)
REVERT: B   74 GLU cc_start: 0.9356 (pp20) cc_final: 0.8987 (pp20)
REVERT: B   84 MET cc_start: 0.8614 (tpt) cc_final: 0.8234 (tpp)
REVERT: D   37 TYR cc_start: 0.9350 (m-80) cc_final: 0.8892 (m-80)
REVERT: D   68 ASP cc_start: 0.9238 (m-30) cc_final: 0.8855 (m-30)
REVERT: D   86 ARG cc_start: 0.9275 (mmp80) cc_final: 0.8752 (mmp80)
REVERT: E   97 GLU cc_start: 0.9430 (mt-10) cc_final: 0.8819 (mm-30)
REVERT: E  110 CYS cc_start: 0.9677 (m) cc_final: 0.9153 (t)
REVERT: F   70 VAL cc_start: 0.9738 (m) cc_final: 0.9515 (m)
REVERT: F   74 GLU cc_start: 0.9045 (pp20) cc_final: 0.8498 (pp20)
REVERT: F   84 MET cc_start: 0.8647 (tpp) cc_final: 0.8329 (tpp)
REVERT: F   87 VAL cc_start: 0.9444 (t) cc_final: 0.9186 (t)
REVERT: F   93 GLN cc_start: 0.8851 (tt0) cc_final: 0.8620 (tm-30)
REVERT: G   38 ASN cc_start: 0.9076 (m-40) cc_final: 0.8763 (p0)
REVERT: G   39 TYR cc_start: 0.9202 (m-80) cc_final: 0.8765 (m-80)
REVERT: N 1349 MET cc_start: 0.6000 (tpt) cc_final: 0.5757 (tpt)
  outliers start: 2
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1098
  time to fit residues: 24.2232
Evaluate side-chains
  100 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 114 optimal weight:   20.0000
   chunk 21 optimal weight:    0.9990
   chunk 1 optimal weight:    9.9990
   chunk 61 optimal weight:    2.9990
   chunk 104 optimal weight:    0.0170
   chunk 10 optimal weight:    0.9980
   chunk 116 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 94 optimal weight:    5.9990
   overall best weight:    1.2024

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

Flipped N/Q/H residues before XYZ refinement:
D 109 HIS
E  93 GLN
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.061977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.039866 restraints weight = 154335.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.040926 restraints weight = 78658.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.041662 restraints weight = 52419.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.041944 restraints weight = 41623.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.042153 restraints weight = 37497.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.5140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  17266  Z= 0.159
  Angle     :  0.602  10.302  24572  Z= 0.344
  Chirality :  0.036   0.147   2738
  Planarity :  0.004   0.065   2114
  Dihedral  : 29.833 179.957   4715
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.07 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.23), residues: 1256
  helix:  1.51 (0.18), residues: 760
  sheet: -0.03 (0.72), residues: 55
  loop : -0.31 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  79 
 TYR   0.018   0.001   TYR D 121 
 PHE   0.029   0.001   PHE E 104 
 TRP   0.017   0.002   TRP N1436 
 HIS   0.004   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (17266)
  covalent geometry    : angle       0.60192 (24572)
  hydrogen bonds       : bond        0.04486 (  831)
  hydrogen bonds       : angle       3.66624 ( 2214)

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9041 (tt0) cc_final: 0.8609 (pt0)
REVERT: A   97 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8177 (mp0)
REVERT: A  105 GLU cc_start: 0.9301 (mm-30) cc_final: 0.9076 (mm-30)
REVERT: A  110 CYS cc_start: 0.8758 (t) cc_final: 0.8454 (t)
REVERT: B   44 LYS cc_start: 0.8674 (pptt) cc_final: 0.8369 (pptt)
REVERT: B   74 GLU cc_start: 0.9308 (pp20) cc_final: 0.8911 (pp20)
REVERT: D   65 PHE cc_start: 0.9745 (t80) cc_final: 0.9441 (t80)
REVERT: D   68 ASP cc_start: 0.9220 (m-30) cc_final: 0.8862 (m-30)
REVERT: D  121 TYR cc_start: 0.9056 (t80) cc_final: 0.8818 (t80)
REVERT: E   90 MET cc_start: 0.9138 (mmp) cc_final: 0.8797 (mmm)
REVERT: E   97 GLU cc_start: 0.9447 (mt-10) cc_final: 0.8871 (mm-30)
REVERT: E  110 CYS cc_start: 0.9694 (m) cc_final: 0.9120 (t)
REVERT: F   62 LEU cc_start: 0.9737 (mt) cc_final: 0.9530 (mp)
REVERT: F   63 GLU cc_start: 0.9336 (mt-10) cc_final: 0.8570 (mp0)
REVERT: F   70 VAL cc_start: 0.9735 (m) cc_final: 0.9497 (m)
REVERT: F   74 GLU cc_start: 0.9042 (pp20) cc_final: 0.8470 (pp20)
REVERT: F   84 MET cc_start: 0.8573 (tpp) cc_final: 0.8342 (tpp)
REVERT: F   87 VAL cc_start: 0.9510 (t) cc_final: 0.9287 (t)
REVERT: F   93 GLN cc_start: 0.8843 (tt0) cc_final: 0.8613 (tm-30)
REVERT: G   38 ASN cc_start: 0.9048 (m-40) cc_final: 0.8722 (p0)
REVERT: G   39 TYR cc_start: 0.9116 (m-80) cc_final: 0.8464 (m-80)
REVERT: G   64 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8883 (mm-30)
REVERT: H   41 VAL cc_start: 0.9523 (t) cc_final: 0.8945 (t)
REVERT: H   62 MET cc_start: 0.9504 (tpp) cc_final: 0.8851 (ptt)
REVERT: N 1349 MET cc_start: 0.5699 (tpt) cc_final: 0.5232 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 152
  average time/residue: 0.1220
  time to fit residues: 27.6650
Evaluate side-chains
  107 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 45 optimal weight:   50.0000
   chunk 49 optimal weight:    1.9990
   chunk 43 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 70 optimal weight:    0.8980
   chunk 94 optimal weight:    5.9990
   chunk 75 optimal weight:    7.9990
   chunk 88 optimal weight:    8.9990
   chunk 67 optimal weight:    0.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.061829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.039797 restraints weight = 154616.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.040868 restraints weight = 79255.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.041582 restraints weight = 52525.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.041850 restraints weight = 41924.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.041918 restraints weight = 37780.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.5319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  17266  Z= 0.169
  Angle     :  0.612  10.282  24572  Z= 0.350
  Chirality :  0.036   0.179   2738
  Planarity :  0.004   0.062   2114
  Dihedral  : 29.715 179.786   4715
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.72 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.23), residues: 1256
  helix:  1.42 (0.18), residues: 766
  sheet:  0.02 (0.72), residues: 55
  loop : -0.27 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  79 
 TYR   0.042   0.002   TYR F  88 
 PHE   0.015   0.001   PHE A  67 
 TRP   0.016   0.001   TRP N1436 
 HIS   0.004   0.001   HIS N1255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (17266)
  covalent geometry    : angle       0.61155 (24572)
  hydrogen bonds       : bond        0.04758 (  831)
  hydrogen bonds       : angle       3.74727 ( 2214)

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.9294 (mm-30) cc_final: 0.9071 (mm-30)
REVERT: A  110 CYS cc_start: 0.8894 (t) cc_final: 0.8537 (t)
REVERT: B   44 LYS cc_start: 0.8687 (pptt) cc_final: 0.8351 (pptt)
REVERT: B   63 GLU cc_start: 0.9199 (pm20) cc_final: 0.8892 (pm20)
REVERT: B   74 GLU cc_start: 0.9301 (pp20) cc_final: 0.8899 (pp20)
REVERT: B   84 MET cc_start: 0.8698 (tpt) cc_final: 0.8400 (tpp)
REVERT: D   68 ASP cc_start: 0.9159 (m-30) cc_final: 0.8793 (m-30)
REVERT: E   90 MET cc_start: 0.9116 (mmp) cc_final: 0.8745 (mmm)
REVERT: E   97 GLU cc_start: 0.9445 (mt-10) cc_final: 0.8894 (mm-30)
REVERT: E  110 CYS cc_start: 0.9696 (m) cc_final: 0.9147 (t)
REVERT: E  120 MET cc_start: 0.8157 (mmm) cc_final: 0.7846 (mmm)
REVERT: F   63 GLU cc_start: 0.9338 (mt-10) cc_final: 0.8693 (mt-10)
REVERT: F   70 VAL cc_start: 0.9739 (m) cc_final: 0.9504 (m)
REVERT: F   74 GLU cc_start: 0.9062 (pp20) cc_final: 0.8512 (pp20)
REVERT: F   88 TYR cc_start: 0.8377 (m-10) cc_final: 0.8176 (m-10)
REVERT: F   93 GLN cc_start: 0.8992 (tt0) cc_final: 0.8639 (tm-30)
REVERT: G   38 ASN cc_start: 0.9043 (m-40) cc_final: 0.8699 (p0)
REVERT: G   39 TYR cc_start: 0.9185 (m-80) cc_final: 0.8486 (m-80)
REVERT: G   64 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8825 (mm-30)
REVERT: G   99 ARG cc_start: 0.7689 (tpt90) cc_final: 0.7355 (mmm160)
REVERT: G  100 VAL cc_start: 0.8977 (t) cc_final: 0.8776 (t)
  outliers start: 1
  outliers final: 1
  residues processed: 142
  average time/residue: 0.1052
  time to fit residues: 22.4912
Evaluate side-chains
  104 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 77 optimal weight:    5.9990
   chunk 69 optimal weight:    8.9990
   chunk 121 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 55 optimal weight:    0.5980
   chunk 31 optimal weight:    5.9990
   chunk 85 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 99 optimal weight:    7.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    3.1186

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

Flipped N/Q/H residues before XYZ refinement:
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N1173 GLN
** N1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N1659 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.059652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.037930 restraints weight = 158570.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.038958 restraints weight = 82946.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.039539 restraints weight = 55578.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.039940 restraints weight = 45288.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.040007 restraints weight = 40233.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.5847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  17266  Z= 0.234
  Angle     :  0.655  10.992  24572  Z= 0.374
  Chirality :  0.038   0.183   2738
  Planarity :  0.005   0.074   2114
  Dihedral  : 29.962 179.739   4715
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.22), residues: 1256
  helix:  1.31 (0.18), residues: 763
  sheet: -0.20 (0.71), residues: 55
  loop : -0.35 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  79 
 TYR   0.039   0.002   TYR F  88 
 PHE   0.013   0.002   PHE D  65 
 TRP   0.016   0.002   TRP N1436 
 HIS   0.006   0.001   HIS F  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 (17266)
  covalent geometry    : angle       0.65547 (24572)
  hydrogen bonds       : bond        0.06608 (  831)
  hydrogen bonds       : angle       4.04287 ( 2214)

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9507 (mm-30) cc_final: 0.9141 (mm-30)
REVERT: A   94 GLU cc_start: 0.8848 (pt0) cc_final: 0.8575 (pt0)
REVERT: A   97 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8160 (mp0)
REVERT: A  110 CYS cc_start: 0.8941 (t) cc_final: 0.8652 (t)
REVERT: B   63 GLU cc_start: 0.9204 (pm20) cc_final: 0.8947 (pm20)
REVERT: B   74 GLU cc_start: 0.9311 (pp20) cc_final: 0.8893 (pp20)
REVERT: C   89 ASN cc_start: 0.9414 (m-40) cc_final: 0.9190 (m-40)
REVERT: D   68 ASP cc_start: 0.9140 (m-30) cc_final: 0.8761 (m-30)
REVERT: D   86 ARG cc_start: 0.9265 (mmp80) cc_final: 0.8942 (mmp80)
REVERT: E   90 MET cc_start: 0.9113 (mmp) cc_final: 0.8810 (mmm)
REVERT: E   97 GLU cc_start: 0.9376 (mt-10) cc_final: 0.8885 (mm-30)
REVERT: E  110 CYS cc_start: 0.9674 (m) cc_final: 0.9162 (t)
REVERT: E  120 MET cc_start: 0.8302 (mmm) cc_final: 0.8031 (mmm)
REVERT: F   63 GLU cc_start: 0.9320 (mt-10) cc_final: 0.8652 (mt-10)
REVERT: F   70 VAL cc_start: 0.9733 (m) cc_final: 0.9507 (m)
REVERT: F   74 GLU cc_start: 0.9054 (pp20) cc_final: 0.8511 (pp20)
REVERT: F   87 VAL cc_start: 0.9547 (t) cc_final: 0.9293 (t)
REVERT: F   88 TYR cc_start: 0.8484 (m-10) cc_final: 0.8115 (m-10)
REVERT: F   93 GLN cc_start: 0.8899 (tt0) cc_final: 0.8691 (tm-30)
REVERT: G   38 ASN cc_start: 0.9080 (m-40) cc_final: 0.8754 (p0)
REVERT: G   39 TYR cc_start: 0.9252 (m-80) cc_final: 0.8587 (m-80)
REVERT: G   64 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8774 (mm-30)
REVERT: G   99 ARG cc_start: 0.7797 (tpt90) cc_final: 0.7418 (mmm160)
REVERT: H   41 VAL cc_start: 0.9490 (t) cc_final: 0.9266 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1240
  time to fit residues: 25.6962
Evaluate side-chains
  102 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 130 optimal weight:    0.0370
   chunk 131 optimal weight:   20.0000
   chunk 92 optimal weight:    6.9990
   chunk 57 optimal weight:    0.0870
   chunk 127 optimal weight:    6.9990
   chunk 148 optimal weight:    6.9990
   chunk 88 optimal weight:    7.9990
   chunk 18 optimal weight:    6.9990
   chunk 102 optimal weight:    9.9990
   chunk 27 optimal weight:    2.9990
   chunk 103 optimal weight:    7.9990
   overall best weight:    3.4242

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N1638 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.059103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.037453 restraints weight = 158008.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 73)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.038406 restraints weight = 83330.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.039007 restraints weight = 56599.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.039246 restraints weight = 45464.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.039302 restraints weight = 41349.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.6350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  17266  Z= 0.237
  Angle     :  0.669  10.582  24572  Z= 0.381
  Chirality :  0.039   0.169   2738
  Planarity :  0.005   0.075   2114
  Dihedral  : 30.265 175.567   4715
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 15.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.22), residues: 1256
  helix:  1.18 (0.18), residues: 762
  sheet: -0.49 (0.67), residues: 59
  loop : -0.36 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  79 
 TYR   0.036   0.002   TYR F  88 
 PHE   0.020   0.002   PHE D  65 
 TRP   0.018   0.002   TRP N1436 
 HIS   0.006   0.001   HIS F  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 (17266)
  covalent geometry    : angle       0.66886 (24572)
  hydrogen bonds       : bond        0.06184 (  831)
  hydrogen bonds       : angle       4.15177 ( 2214)

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9499 (mm-30) cc_final: 0.9176 (mm-30)
REVERT: A   94 GLU cc_start: 0.8867 (pt0) cc_final: 0.8431 (tt0)
REVERT: A  105 GLU cc_start: 0.9258 (mm-30) cc_final: 0.9047 (mm-30)
REVERT: A  110 CYS cc_start: 0.9007 (t) cc_final: 0.8709 (t)
REVERT: B   74 GLU cc_start: 0.9299 (pp20) cc_final: 0.8906 (pp20)
REVERT: B   84 MET cc_start: 0.8356 (tpt) cc_final: 0.8132 (tpp)
REVERT: C   56 GLU cc_start: 0.9220 (pm20) cc_final: 0.9016 (pm20)
REVERT: C  112 GLN cc_start: 0.9109 (mp10) cc_final: 0.8782 (mp10)
REVERT: D   67 ASN cc_start: 0.9235 (m-40) cc_final: 0.8588 (m-40)
REVERT: D   68 ASP cc_start: 0.9176 (m-30) cc_final: 0.8840 (m-30)
REVERT: E   90 MET cc_start: 0.9135 (mmp) cc_final: 0.8841 (mmm)
REVERT: E   97 GLU cc_start: 0.9396 (mt-10) cc_final: 0.8924 (mm-30)
REVERT: E  110 CYS cc_start: 0.9676 (m) cc_final: 0.9188 (t)
REVERT: E  120 MET cc_start: 0.8484 (mmm) cc_final: 0.8253 (mmm)
REVERT: F   70 VAL cc_start: 0.9743 (m) cc_final: 0.9511 (m)
REVERT: F   74 GLU cc_start: 0.9063 (pp20) cc_final: 0.8496 (pp20)
REVERT: F   87 VAL cc_start: 0.9555 (t) cc_final: 0.9295 (t)
REVERT: F   88 TYR cc_start: 0.8494 (m-10) cc_final: 0.8125 (m-10)
REVERT: F   93 GLN cc_start: 0.9059 (tt0) cc_final: 0.8778 (tm-30)
REVERT: G   38 ASN cc_start: 0.9085 (m-40) cc_final: 0.8800 (p0)
REVERT: G   39 TYR cc_start: 0.9233 (m-80) cc_final: 0.8552 (m-80)
REVERT: G   64 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8741 (mm-30)
REVERT: G   74 LYS cc_start: 0.9455 (mmmt) cc_final: 0.9223 (mmmt)
REVERT: G   99 ARG cc_start: 0.7751 (tpt90) cc_final: 0.7396 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1203
  time to fit residues: 24.3620
Evaluate side-chains
  100 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 69 optimal weight:    7.9990
   chunk 84 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 98 optimal weight:    6.9990
   chunk 30 optimal weight:    0.8980
   chunk 73 optimal weight:   20.0000
   chunk 138 optimal weight:    6.9990
   chunk 77 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.060278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.038420 restraints weight = 155665.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.039462 restraints weight = 80829.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.040130 restraints weight = 54540.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.040344 restraints weight = 43914.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.040538 restraints weight = 40048.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.6366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  17266  Z= 0.174
  Angle     :  0.654  14.941  24572  Z= 0.365
  Chirality :  0.037   0.200   2738
  Planarity :  0.004   0.073   2114
  Dihedral  : 30.183 175.415   4715
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.23), residues: 1256
  helix:  1.26 (0.18), residues: 761
  sheet: -0.52 (0.67), residues: 59
  loop : -0.32 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  79 
 TYR   0.031   0.002   TYR F  88 
 PHE   0.011   0.001   PHE A  67 
 TRP   0.017   0.002   TRP N1436 
 HIS   0.004   0.001   HIS N1255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (17266)
  covalent geometry    : angle       0.65360 (24572)
  hydrogen bonds       : bond        0.04854 (  831)
  hydrogen bonds       : angle       3.98144 ( 2214)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2923.88 seconds
wall clock time: 51 minutes 8.45 seconds (3068.45 seconds total)